!qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path Data/raw_data/ \
--input-format CasavaOneEightSingleLanePerSampleDirFmt \
--output-path Data/demux-paired-end.qza
!qiime demux summarize \
--i-data Data/demux-paired-end.qza \
--o-visualization Results/demux-paired-end.qzv
!qiime cutadapt trim-paired \
--i-demultiplexed-sequences Data/demux-paired-end.qza \
--o-trimmed-sequences Data/trimmed-paired-end.qza \
--p-cores 18 \
--p-front-f AGATGTGTATAAGAGACAGCCTACGGGNGGCNGCAG \
--p-front-r GACTACNNGGGTATCTAATCC \
--p-match-adapter-wildcards
# Visualization
!mkdir Results
!qiime demux summarize \
--i-data Data/trimmed-paired-end.qza \
--o-visualization Results/trimmed-paired-end.qzv
Note. We modified R script for Dada2 (file "anaconda3/envs/qiime2-2019.4/bin/run_dada_paired.R") by providing “mergers[[j]] <- mergePairs(ddF, drpF, ddR, drpR, minOverlap=4)” to allow change minimum overlap to 4
!mkdir Data/tables
!qiime dada2 denoise-paired \
--i-demultiplexed-seqs Data/trimmed-paired-end.qza \
--p-trim-left-f 2 \
--p-trim-left-r 2 \
--p-trunc-len-f 267 \
--p-trunc-len-r 238 \
--p-n-threads 18 \
--o-table Data/tables/table.qza \
--o-representative-sequences Data/rep-seqs.qza \
--o-denoising-stats Data/denoising-stats.qza
!qiime feature-table tabulate-seqs \
--i-data Data/rep-seqs.qza \
--o-visualization Results/rep-seqs.qzv
!qiime metadata tabulate \
--m-input-file Data/denoising-stats.qza \
--o-visualization Results/denoising-stats.qzv
!mkdir -p Results/tables
!qiime feature-table summarize \
--i-table Data/tables/table.qza \
--o-visualization Results/tables/table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
!rm Data/demux-paired-end.qza Data/trimmed-paired-end.qza
!qiime feature-classifier classify-sklearn \
--i-classifier training-feature-classifiers/classifier.qza \
--i-reads Data/rep-seqs.qza \
--o-classification Data/taxonomy.qza
#--p-reads-per-batch 20000 \
!qiime tools export \
--input-path Data/taxonomy.qza \
--output-path Data/taxonomy-with-spaces
!qiime metadata tabulate \
--m-input-file Data/taxonomy-with-spaces/taxonomy.tsv \
--o-visualization Data/taxonomy-as-metadata.qzv
!qiime tools export \
--input-path Data/taxonomy-as-metadata.qzv \
--output-path Data/taxonomy-as-metadata
!qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-path Data/taxonomy-as-metadata/metadata.tsv \
--output-path Data/taxonomy-without-spaces.qza
!qiime metadata tabulate \
--m-input-file Data/taxonomy-without-spaces.qza \
--o-visualization Results/taxonomy-without-spaces.qzv
!rm -r Data/taxonomy-with-spaces Data/taxonomy-as-metadata
!conda install -y -c anaconda biopython
Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/timyerg/anaconda3/envs/qiime2-2020.2 added / updated specs: - biopython The following packages will be downloaded: package | build ---------------------------|----------------- biopython-1.76 | py36h7b6447c_0 2.6 MB anaconda certifi-2020.4.5.1 | py36_0 159 KB anaconda openssl-1.1.1g | h7b6447c_0 3.8 MB anaconda ------------------------------------------------------------ Total: 6.6 MB The following NEW packages will be INSTALLED: biopython anaconda/linux-64::biopython-1.76-py36h7b6447c_0 The following packages will be SUPERSEDED by a higher-priority channel: ca-certificates conda-forge::ca-certificates-2020.4.5~ --> anaconda::ca-certificates-2020.1.1-0 certifi conda-forge::certifi-2020.4.5.1-py36h~ --> anaconda::certifi-2020.4.5.1-py36_0 openssl conda-forge::openssl-1.1.1g-h516909a_0 --> anaconda::openssl-1.1.1g-h7b6447c_0 Downloading and Extracting Packages openssl-1.1.1g | 3.8 MB | ##################################### | 100% certifi-2020.4.5.1 | 159 KB | ##################################### | 100% biopython-1.76 | 2.6 MB | ##################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done
#input
table = 'Data/tables/table.qza'
taxa = 'Data/taxonomy-without-spaces.qza'
rep_seq = 'Data/rep-seqs.qza'
#import
import pandas as pd
from Bio import SeqIO
#export rep-seqs.qza, table.qza and taxonomy.qza
!mkdir Biom Taxa Rep-seqs
!qiime tools export \
--input-path $table \
--output-path Biom/
!biom convert -i Biom/feature-table.biom -o Biom/feature-table.tsv --to-tsv
!qiime tools export \
--input-path $taxa \
--output-path Taxa
!qiime tools export \
--input-path $rep_seq \
--output-path Rep-seqs/
#replacing hashes with combination of taxonomy and beginings of the hashes
taxa_df = pd.read_csv('Taxa/taxonomy.tsv', sep='\t', skiprows=[1])
biom_df = pd.read_csv('Biom/feature-table.tsv', sep='\t', skiprows=1)
taxa_df['Combo'] = pd.DataFrame(taxa_df['Taxon'].astype(str).str.replace(';__', '').str.replace('[', '').str.replace(']', '')
.str.replace('.', '').str.replace('/', '_').str.replace("'", '').str.replace(' ', '_')
.str.split("__").str[-1].str.split(";").str[-1])
for n in range(2,7):
taxa_df.loc[taxa_df['Combo'].str.contains('uncultured_bacterium'),'Combo'] = taxa_df['Taxon'].astype(str)\
.str.replace(';__','').str.replace('[','').str.replace(']','').str.replace('.','').str.replace('/','_')\
.str.replace("'",'').str.replace(' ','_').str.split("__").str[-n].str.split(';').str[0]+'_unc_b'
taxa_df.loc[taxa_df['Combo'].str.contains('uncultured'),'Combo'] = taxa_df['Taxon'].astype(str)\
.str.replace(';__','').str.replace('[','').str.replace(']','').str.replace('.','').str.replace('/','_')\
.str.replace("'",'').str.replace(' ','_').str.split("__").str[-n].str.split(';').str[0]+'_unc'
biom_df['#OTU ID'] = taxa_df['Combo']+'|'+taxa_df['Feature ID']
taxa_df['Feature ID'] = biom_df['#OTU ID']
taxa_df = taxa_df[['Feature ID', 'Taxon', 'Confidence']]
#writing all files back
biom_df.to_csv('Biom/feature-table.tsv', sep='\t', index=False)
taxa_df.to_csv('Taxa/taxonomy.tsv', sep='\t', index=False)
fasta_hash = r"Rep-seqs/dna-sequences.fasta"
fasta_combo = r"Rep-seqs/dna-sequences.fa"
i=0
with open(fasta_hash) as hashes, open(fasta_combo, 'w') as combo:
records = SeqIO.parse(fasta_hash, 'fasta')
for record in records:
record.id = biom_df['#OTU ID'][i]
record.description = ''
i+=1
SeqIO.write(record, combo, 'fasta')
!rm $fasta_hash
!mv $fasta_combo $fasta_hash
Exported Data/tables/table.qza as BIOMV210DirFmt to directory Biom/ Exported Data/taxonomy-without-spaces.qza as TSVTaxonomyDirectoryFormat to directory Taxa Exported Data/rep-seqs.qza as DNASequencesDirectoryFormat to directory Rep-seqs/
#creating new rep-seqs.qza, table.qza and taxonomy.qza with modified hashes
!biom convert -i Biom/feature-table.tsv -o Biom/feature-table.biom --table-type="OTU table" --to-hdf5
!qiime tools import \
--input-path Biom/feature-table.biom \
--type 'FeatureTable[Frequency]' \
--input-format BIOMV210Format \
--output-path Data/tables/combo_table.qza
!qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-path Taxa/taxonomy.tsv \
--output-path Data/combo_taxonomy.qza
!qiime tools import \
--input-path $fasta_hash \
--output-path Data/combo_rep-seqs.qza \
--type 'FeatureData[Sequence]'
!rm -r Biom Taxa Rep-seqs
Imported Biom/feature-table.biom as BIOMV210Format to Data/tables/combo_table.qza Imported Taxa/taxonomy.tsv as TSVTaxonomyDirectoryFormat to Data/combo_taxonomy.qza Imported Rep-seqs/dna-sequences.fasta as DNASequencesDirectoryFormat to Data/combo_rep-seqs.qza
!qiime phylogeny align-to-tree-mafft-fasttree \
--i-sequences Data/combo_rep-seqs.qza \
--o-alignment Data/aligned-rep-seqs.qza \
--o-masked-alignment Data/masked-aligned-rep-seqs.qza \
--o-tree Data/unrooted-tree.qza \
--o-rooted-tree Data/rooted-tree.qza \
--p-n-threads 18
Saved FeatureData[AlignedSequence] to: Data/aligned-rep-seqs.qza Saved FeatureData[AlignedSequence] to: Data/masked-aligned-rep-seqs.qza Saved Phylogeny[Unrooted] to: Data/unrooted-tree.qza Saved Phylogeny[Rooted] to: Data/rooted-tree.qza
!qiime feature-table filter-features \
--i-table Data/tables/combo_table.qza \
--p-min-frequency 10 \
--p-min-samples 5 \
--o-filtered-table Data/tables/sample-contingency-filtered-table.qza
!qiime taxa filter-table \
--i-table Data/tables/sample-contingency-filtered-table.qza \
--i-taxonomy Data/combo_taxonomy.qza \
--p-exclude mitochondria,chloroplast \
--o-filtered-table Data/tables/table-no-mit_chlor.qza
!qiime feature-table filter-samples \
--i-table Data/tables/table-no-mit_chlor.qza \
--p-min-features 25 \
--p-min-frequency 8000 \
--o-filtered-table Data/tables/filtered-table.qza
!qiime feature-table filter-samples \
--i-table Data/tables/filtered-table.qza \
--m-metadata-file Data/tables/samples_to_exclude.tsv \
--p-exclude-ids \
--o-filtered-table Data/tables/filtered-table.qza
!mkdir Results/tables
!qiime feature-table summarize \
--i-table Data/tables/filtered-table.qza \
--o-visualization Results/tables/filtered-table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
Saved FeatureTable[Frequency] to: Data/tables/table-no-mit_chlor.qza Saved FeatureTable[Frequency] to: Data/tables/filtered-table.qza Saved FeatureTable[Frequency] to: Data/tables/filtered-table.qza Saved Visualization to: Results/tables/filtered-table.qzv
Extracted manually a taxonomy.tsv file from combo_taxonomy.qza and filtered it to leave only features to exclude.
!qiime feature-table filter-features \
--i-table Data/tables/filtered-table.qza \
--m-metadata-file Data/tables/taxonomy_to_exclude.tsv \
--p-exclude-ids \
--o-filtered-table Data/tables/All_table.qza
!qiime feature-table summarize \
--i-table Data/tables/All_table.qza \
--o-visualization Results/tables/All_table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
Saved FeatureTable[Frequency] to: Data/tables/All_table.qza Saved Visualization to: Results/tables/All_table.qzv
!qiime feature-table filter-samples \
--i-table Data/tables/All_table.qza \
--m-metadata-file Metadata/metadata.tsv \
--p-where "Treatment='Infected'" \
--o-filtered-table Data/tables/Infected_table.qza
!qiime feature-table summarize \
--i-table Data/tables/Infected_table.qza \
--o-visualization Results/tables/Infected_table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
Saved FeatureTable[Frequency] to: Data/tables/Infected_table.qza Saved Visualization to: Results/tables/Infected_table.qzv
#Filtering by Niche
Niche_list = ['Root', 'Gall', 'J2', 'Soil']
for Niche in Niche_list:
tabin = 'Data/tables/Infected_table.qza'
tabout = 'Data/tables/%s_table.qza' % Niche
column = "Niche='%s'" % Niche
!qiime feature-table filter-samples \
--i-table $tabin \
--m-metadata-file Metadata/metadata.tsv \
--p-where "$column" \
--o-filtered-table $tabout
!qiime feature-table filter-features \
--i-table $tabout \
--p-min-frequency 3 \
--p-min-samples 3 \
--o-filtered-table $tabout
Saved FeatureTable[Frequency] to: Data/tables/Root_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_table.qza
import itertools
Niche_list = ['Root', 'Gall', 'J2', 'Soil']
for Niche_1, Niche_2 in itertools.combinations(Niche_list, 2):
tabin = 'Data/tables/Infected_table.qza'
tabout = 'Data/tables/%s-%s_table.qza' % (Niche_1, Niche_2)
column = "Niche IN ('%s','%s')" % (Niche_1, Niche_2)
!qiime feature-table filter-samples \
--i-table $tabin \
--m-metadata-file Metadata/metadata.tsv \
--p-where "$column" \
--o-filtered-table $tabout
!qiime feature-table filter-features \
--i-table $tabout \
--p-min-frequency 3 \
--p-min-samples 3 \
--o-filtered-table $tabout
tps = [1, 2, 3, 4, 5, 6]
if Niche_1 == 'Gall' or Niche_2 == 'Gall':
tps = [2, 3, 4, 5, 6]
if Niche_1 == 'J2' or Niche_2 == 'J2':
tps = [2, 3, 4, 6]
for tp in tps:
tab_tp = 'Data/tables/%s-%s_%s_table.qza' % (Niche_1, Niche_2, tp)
col = "TimePoint='%s'" % tp
!qiime feature-table filter-samples \
--i-table $tabout \
--m-metadata-file Metadata/metadata.tsv \
--p-where "$col" \
--o-filtered-table $tab_tp
!qiime feature-table filter-features \
--i-table $tab_tp \
--p-min-frequency 2 \
--p-min-samples 2 \
--o-filtered-table $tab_tp
Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Gall_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-J2_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_1_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_1_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root-Soil_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-J2_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall-Soil_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_2_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_3_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_4_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2-Soil_6_table.qza
import itertools
Niche_list = ['Root', 'Gall', 'J2', 'Soil']
for Niche in Niche_list:
if Niche == 'Gall':
tps = [2, 3, 4, 5, 6]
if Niche == 'J2':
tps = [2, 3, 4, 6]
else:
tps = [1, 2, 3, 4, 5, 6]
for tp_1, tp_2 in itertools.combinations(tps, 2):
tabin = 'Data/tables/%s_table.qza' % Niche
tabout = 'Data/tables/%s_%s-%s_table.qza' % (Niche, tp_1, tp_2)
column = "TimePoint IN ('%s','%s')" % (tp_1, tp_2)
!qiime feature-table filter-samples \
--i-table $tabin \
--m-metadata-file Metadata/metadata.tsv \
--p-where "$column" \
--o-filtered-table $tabout
!qiime feature-table filter-features \
--i-table $tabout \
--p-min-frequency 2 \
--p-min-samples 2 \
--o-filtered-table $tabout
Saved FeatureTable[Frequency] to: Data/tables/Root_1-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_1-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_3-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_3-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_4-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_4-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_5-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Root_5-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_1-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_3-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_3-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_4-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_4-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_5-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Gall_5-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/J2_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_1-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_2-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_3-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_3-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_3-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_3-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_4-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_4-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_4-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_5-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_5-6_table.qza
#Filtering by TimePoint
for TP in range(1,7):
tabin = 'Data/tables/Infected_table.qza'
tabout = 'Data/tables/tp-%s_table.qza' % TP
column = "TimePoint='%s'" % TP
!qiime feature-table filter-samples \
--i-table $tabin \
--m-metadata-file Metadata/metadata.tsv \
--p-where "$column" \
--o-filtered-table $tabout
!qiime feature-table filter-features \
--i-table $tabout \
--p-min-frequency 2 \
--p-min-samples 2 \
--o-filtered-table $tabout
import itertools
Niche_list = ['Root', 'Gall', 'J2', 'Soil']
for Niche_1, Niche_2 in itertools.combinations(Niche_list, 2):
for TP in range(1,7):
tabin = 'Data/tables/%s-%s_table.qza' % (Niche_1, Niche_2)
tabout = 'Data/tables/tp-%s-%s-%s_table.qza' % (TP, Niche_1, Niche_2)
column = "TimePoint='%s'" % TP
!qiime feature-table filter-samples \
--i-table $tabin \
--m-metadata-file Metadata/metadata.tsv \
--p-where "$column" \
--o-filtered-table $tabout
!qiime feature-table filter-features \
--i-table $tabout \
--p-min-frequency 2 \
--p-min-samples 2 \
--o-filtered-table $tabout
Saved FeatureTable[Frequency] to: Data/tables/tp-1_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Root-Gall_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Root-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Root-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Gall-J2_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-Gall-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-1-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-2-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-3-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-4-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-5-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-J2-Soil_table.qza Saved FeatureTable[Frequency] to: Data/tables/tp-6-J2-Soil_table.qza
import pandas as pd
outdir = 'Results/Taxa_barplots'
tabin = 'Data/tables/Infected_table.qza'
groups = ['Group_TP','Niche']#, 'Group_Treat']
meta = pd.read_csv('Metadata/metadata.tsv',sep='\t',index_col=0)
!mkdir -p $outdir
for group in groups:
#Collapse metadata
meta.index = meta[group]
meta = meta.drop_duplicates(subset=group)
meta.index.name = '#SampleID'
meta.to_csv('Metadata/%s_metadata.tsv'%group,sep='\t')
#Variables
grouped = 'Data/tables/Infected_%s_grouped.qza' % group
taxabar = outdir + '/%s_taxabarplot.qzv' % group
metadata= 'Metadata/%s_metadata.tsv' % group
#Group tables
!qiime feature-table group \
--i-table $tabin \
--p-axis 'sample' \
--m-metadata-file Metadata/metadata.tsv \
--m-metadata-column $group \
--p-mode 'mean-ceiling' \
--o-grouped-table $grouped
#Taxabarplots
!qiime taxa barplot \
--i-table $grouped \
--i-taxonomy Data/combo_taxonomy.qza \
--m-metadata-file $metadata \
--o-visualization $taxabar
!qiime taxa barplot \
--i-table Data/tables/Infected_table.qza \
--i-taxonomy Data/combo_taxonomy.qza \
--m-metadata-file Metadata/metadata.tsv \
--o-visualization Results/Taxa_barplots/Infected_taxabarplot.qzv
Saved FeatureTable[Frequency] to: Data/tables/Infected_Group_TP_grouped.qza Saved Visualization to: Results/Taxa_barplots/Group_TP_taxabarplot.qzv Saved FeatureTable[Frequency] to: Data/tables/Infected_Niche_grouped.qza Saved Visualization to: Results/Taxa_barplots/Niche_taxabarplot.qzv Saved Visualization to: Results/Taxa_barplots/Infected_taxabarplot.qzv
# Alpha rarefaction plotting
outdir = 'Results/Core-metrics_analysis'
!mkdir $outdir
variants = ['Infected'] #,"All",'Root-Gall']
for variant in variants:
depth = 15000
alpha = outdir+'/%s_alpha-rarefaction.qzv' % variant
tabin = 'Data/tables/%s_table.qza' % variant
!qiime diversity alpha-rarefaction \
--i-table $tabin \
--i-phylogeny Data/rooted-tree.qza \
--p-max-depth $depth \
--m-metadata-file Metadata/metadata.tsv \
--o-visualization $alpha
mkdir: cannot create directory ‘Results/Core-metrics_analysis’: File exists
Saved Visualization to: Results/Core-metrics_analysis/Infected_alpha-rarefaction.qzv
# core-metrics-phylogenetic: Core diversity metrics (phylogenetic and non-phylogenetic)
!mkdir Data/Core-metrics_analysis
variants = ['Root-Gall', 'Infected']
for variant in variants:
Data_core = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant
Rslt_core = 'Results/Core-metrics_analysis/%s_Core-metrics' % variant
tabin = 'Data/tables/%s_table.qza' % variant
!mkdir $Rslt_core
!qiime diversity core-metrics-phylogenetic \
--i-phylogeny Data/rooted-tree.qza \
--i-table $tabin \
--p-sampling-depth 8828 \
--m-metadata-file Metadata/metadata.tsv \
--p-n-jobs 16 \
--o-unweighted-unifrac-emperor $Rslt_core/unweighted-unifrac-emperor.qzv \
--o-weighted-unifrac-emperor $Rslt_core/weighted-unifrac-emperor.qzv \
--o-jaccard-emperor $Rslt_core/jaccard-emperor.qzv \
--o-bray-curtis-emperor $Rslt_core/bray-curtis-emperor.qzv \
--output-dir $Data_core
Saved FeatureTable[Frequency] to: Data/Core-metrics_analysis/All_Core-metrics/rarefied_table.qza Saved SampleData[AlphaDiversity] % Properties('phylogenetic') to: Data/Core-metrics_analysis/All_Core-metrics/faith_pd_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/All_Core-metrics/observed_otus_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/All_Core-metrics/shannon_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/All_Core-metrics/evenness_vector.qza Saved DistanceMatrix % Properties('phylogenetic') to: Data/Core-metrics_analysis/All_Core-metrics/unweighted_unifrac_distance_matrix.qza Saved DistanceMatrix % Properties('phylogenetic') to: Data/Core-metrics_analysis/All_Core-metrics/weighted_unifrac_distance_matrix.qza Saved DistanceMatrix to: Data/Core-metrics_analysis/All_Core-metrics/jaccard_distance_matrix.qza Saved DistanceMatrix to: Data/Core-metrics_analysis/All_Core-metrics/bray_curtis_distance_matrix.qza Saved PCoAResults to: Data/Core-metrics_analysis/All_Core-metrics/unweighted_unifrac_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/All_Core-metrics/weighted_unifrac_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/All_Core-metrics/jaccard_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/All_Core-metrics/bray_curtis_pcoa_results.qza Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/unweighted-unifrac-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/weighted-unifrac-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/jaccard-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/bray-curtis-emperor.qzv Saved FeatureTable[Frequency] to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/rarefied_table.qza Saved SampleData[AlphaDiversity] % Properties('phylogenetic') to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/faith_pd_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/observed_otus_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/shannon_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/evenness_vector.qza Saved DistanceMatrix % Properties('phylogenetic') to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/unweighted_unifrac_distance_matrix.qza Saved DistanceMatrix % Properties('phylogenetic') to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/weighted_unifrac_distance_matrix.qza Saved DistanceMatrix to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/jaccard_distance_matrix.qza Saved DistanceMatrix to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/bray_curtis_distance_matrix.qza Saved PCoAResults to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/unweighted_unifrac_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/weighted_unifrac_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/jaccard_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/bray_curtis_pcoa_results.qza Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/unweighted-unifrac-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/weighted-unifrac-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/jaccard-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/bray-curtis-emperor.qzv Saved FeatureTable[Frequency] to: Data/Core-metrics_analysis/Infected_Core-metrics/rarefied_table.qza Saved SampleData[AlphaDiversity] % Properties('phylogenetic') to: Data/Core-metrics_analysis/Infected_Core-metrics/faith_pd_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/Infected_Core-metrics/observed_otus_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/Infected_Core-metrics/shannon_vector.qza Saved SampleData[AlphaDiversity] to: Data/Core-metrics_analysis/Infected_Core-metrics/evenness_vector.qza Saved DistanceMatrix % Properties('phylogenetic') to: Data/Core-metrics_analysis/Infected_Core-metrics/unweighted_unifrac_distance_matrix.qza Saved DistanceMatrix % Properties('phylogenetic') to: Data/Core-metrics_analysis/Infected_Core-metrics/weighted_unifrac_distance_matrix.qza Saved DistanceMatrix to: Data/Core-metrics_analysis/Infected_Core-metrics/jaccard_distance_matrix.qza Saved DistanceMatrix to: Data/Core-metrics_analysis/Infected_Core-metrics/bray_curtis_distance_matrix.qza Saved PCoAResults to: Data/Core-metrics_analysis/Infected_Core-metrics/unweighted_unifrac_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/Infected_Core-metrics/weighted_unifrac_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/Infected_Core-metrics/jaccard_pcoa_results.qza Saved PCoAResults to: Data/Core-metrics_analysis/Infected_Core-metrics/bray_curtis_pcoa_results.qza Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/unweighted-unifrac-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/weighted-unifrac-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/jaccard-emperor.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/bray-curtis-emperor.qzv
#Principal Coordinate Analysis Biplot
variants = ['Root-Gall', 'Infected']
for variant in variants:
Data_core = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant
Rslt_core = 'Results/Core-metrics_analysis/%s_Core-metrics' % variant
rel_tab = 'Data/tables/%s_relative_table.qza' % variant
tabin = 'Data/tables/%s_table.qza' % variant
#Converting feature table [Frequency] to [Relative frequency]
!qiime feature-table relative-frequency \
--i-table $tabin \
--o-relative-frequency-table $rel_tab
#pcoa-biplot: Principal Coordinate Analysis Biplot
artifacts = ['unweighted_unifrac', 'weighted_unifrac', 'jaccard', 'bray_curtis']
for artifact in artifacts:
pcoa = Data_core+'/%s_pcoa_results.qza' % artifact
biplot= Data_core+'/%s_biplot.qza' % artifact
bi_qzv= Rslt_core+'/%s_biplot.qzv' % artifact
!qiime diversity pcoa-biplot \
--i-pcoa $pcoa \
--i-features $rel_tab \
--o-biplot $biplot
!qiime emperor biplot \
--i-biplot $biplot \
--m-sample-metadata-file Metadata/metadata.tsv \
--p-ignore-missing-samples \
--p-number-of-features 5 \
--o-visualization $bi_qzv
Saved FeatureTable[RelativeFrequency] to: Data/tables/All_relative_table.qza Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/All_Core-metrics/unweighted_unifrac_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/unweighted_unifrac_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/All_Core-metrics/weighted_unifrac_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/weighted_unifrac_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/All_Core-metrics/jaccard_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/jaccard_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/All_Core-metrics/bray_curtis_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/bray_curtis_biplot.qzv Saved FeatureTable[RelativeFrequency] to: Data/tables/Root-Gall_relative_table.qza Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/unweighted_unifrac_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/unweighted_unifrac_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/weighted_unifrac_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/weighted_unifrac_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/jaccard_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/jaccard_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Root-Gall_Core-metrics/bray_curtis_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/bray_curtis_biplot.qzv Saved FeatureTable[RelativeFrequency] to: Data/tables/Infected_relative_table.qza Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Infected_Core-metrics/unweighted_unifrac_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/unweighted_unifrac_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Infected_Core-metrics/weighted_unifrac_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/weighted_unifrac_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Infected_Core-metrics/jaccard_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/jaccard_biplot.qzv Saved PCoAResults % Properties('biplot') to: Data/Core-metrics_analysis/Infected_Core-metrics/bray_curtis_biplot.qza Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/bray_curtis_biplot.qzv
variants = ['Root-Gall', 'Infected']
for variant in variants:
core = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant
outdir = 'Results/Core-metrics_analysis/%s_Core-metrics' % variant
#Alpha diversity comparisons¶
alpha_diversity = ['shannon', 'faith_pd', 'evenness', 'observed_otus']
for alpha in alpha_diversity:
vector = core+'/%s_vector.qza' % alpha
ags_qzv = outdir+'/%s_vector_alpha-group-sign.qzv' % alpha
!qiime diversity alpha-group-significance \
--i-alpha-diversity $vector \
--m-metadata-file Metadata/metadata.tsv \
--o-visualization $ags_qzv
Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/shannon_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/faith_pd_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/evenness_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/observed_otus_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/shannon_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/faith_pd_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/evenness_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/observed_otus_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/shannon_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/faith_pd_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/evenness_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/observed_otus_vector_alpha-group-sign.qzv
#Beta diversity comparisons¶
variants = ['Root-Gall', 'Infected']
for variant in variants:
core = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant
outdir = 'Results/Core-metrics_analysis/%s_Core-metrics' % variant
beta_diversity = ['unweighted_unifrac', 'weighted_unifrac', 'jaccard', 'bray_curtis']
for beta in beta_diversity:
distance= core+'/%s_distance_matrix.qza' % beta
columns = ['Group_TP', 'Group_Treat']
for column in columns:
bgs_qzv = outdir+'/%s_%s-dist-matrix_beta-group-sign-pairwise.qzv' % (beta, column)
!qiime diversity beta-group-significance \
--i-distance-matrix $distance \
--m-metadata-file Metadata/metadata.tsv \
--m-metadata-column $column \
--p-pairwise \
--o-visualization $bgs_qzv
Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/unweighted_unifrac_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/unweighted_unifrac_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/weighted_unifrac_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/weighted_unifrac_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/jaccard_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/jaccard_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/bray_curtis_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/All_Core-metrics/bray_curtis_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/unweighted_unifrac_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/unweighted_unifrac_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/weighted_unifrac_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/weighted_unifrac_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/jaccard_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/jaccard_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/bray_curtis_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Root-Gall_Core-metrics/bray_curtis_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/unweighted_unifrac_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/unweighted_unifrac_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/weighted_unifrac_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/weighted_unifrac_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/jaccard_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/jaccard_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/bray_curtis_Group_TP-dist-matrix_beta-group-sign-pairwise.qzv Saved Visualization to: Results/Core-metrics_analysis/Infected_Core-metrics/bray_curtis_Group_Treat-dist-matrix_beta-group-sign-pairwise.qzv
#By Niches and TimePoints
outdir= 'Results/Core_Features'
groups = ['S_2','S_3','S_4','S_6',
'R_2','R_3','R_4','R_6',
'G_2','G_3','G_4','G_6',
'J_2','J_3','J_4','J_6']
!mkdir $outdir
for group in groups:
tabin = 'Data/tables/Infected_table.qza'
column = "Group_TP='%s'" % group
tabout = 'Data/tables/%s_table.qza' % group
!qiime feature-table filter-samples \
--i-table $tabin \
--m-metadata-file Metadata/metadata.tsv \
--p-where "$column" \
--o-filtered-table $tabout
table_7= 'Data/tables/%s_7-lev_table.qza' % group
core_7 = outdir+'/%s_7-lev_core.qzv' % group
coreqzv= outdir+'/%s_core.qzv' % group
!qiime taxa collapse \
--i-table $tabout \
--i-taxonomy Data/combo_taxonomy.qza \
--p-level 7 \
--o-collapsed-table $table_7
!qiime feature-table core-features \
--i-table $table_7 \
--o-visualization $core_7
!qiime feature-table core-features \
--i-table $tabout \
--o-visualization $coreqzv
Saved FeatureTable[Frequency] to: Data/tables/S_2_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/S_2_7-lev_table.qza Saved Visualization to: Results/Core_Features/S_2_7-lev_core.qzv Saved Visualization to: Results/Core_Features/S_2_core.qzv Saved FeatureTable[Frequency] to: Data/tables/S_3_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/S_3_7-lev_table.qza Saved Visualization to: Results/Core_Features/S_3_7-lev_core.qzv Saved Visualization to: Results/Core_Features/S_3_core.qzv Saved FeatureTable[Frequency] to: Data/tables/S_4_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/S_4_7-lev_table.qza Saved Visualization to: Results/Core_Features/S_4_7-lev_core.qzv Saved Visualization to: Results/Core_Features/S_4_core.qzv Saved FeatureTable[Frequency] to: Data/tables/S_6_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/S_6_7-lev_table.qza Saved Visualization to: Results/Core_Features/S_6_7-lev_core.qzv Saved Visualization to: Results/Core_Features/S_6_core.qzv Saved FeatureTable[Frequency] to: Data/tables/R_2_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/R_2_7-lev_table.qza Saved Visualization to: Results/Core_Features/R_2_7-lev_core.qzv Saved Visualization to: Results/Core_Features/R_2_core.qzv Saved FeatureTable[Frequency] to: Data/tables/R_3_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/R_3_7-lev_table.qza Saved Visualization to: Results/Core_Features/R_3_7-lev_core.qzv Saved Visualization to: Results/Core_Features/R_3_core.qzv Saved FeatureTable[Frequency] to: Data/tables/R_4_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/R_4_7-lev_table.qza Saved Visualization to: Results/Core_Features/R_4_7-lev_core.qzv Saved Visualization to: Results/Core_Features/R_4_core.qzv Saved FeatureTable[Frequency] to: Data/tables/R_6_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/R_6_7-lev_table.qza Saved Visualization to: Results/Core_Features/R_6_7-lev_core.qzv Saved Visualization to: Results/Core_Features/R_6_core.qzv Saved FeatureTable[Frequency] to: Data/tables/G_2_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/G_2_7-lev_table.qza Saved Visualization to: Results/Core_Features/G_2_7-lev_core.qzv Saved Visualization to: Results/Core_Features/G_2_core.qzv Saved FeatureTable[Frequency] to: Data/tables/G_3_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/G_3_7-lev_table.qza Saved Visualization to: Results/Core_Features/G_3_7-lev_core.qzv Saved Visualization to: Results/Core_Features/G_3_core.qzv Saved FeatureTable[Frequency] to: Data/tables/G_4_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/G_4_7-lev_table.qza Saved Visualization to: Results/Core_Features/G_4_7-lev_core.qzv Saved Visualization to: Results/Core_Features/G_4_core.qzv Saved FeatureTable[Frequency] to: Data/tables/G_6_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/G_6_7-lev_table.qza Saved Visualization to: Results/Core_Features/G_6_7-lev_core.qzv Saved Visualization to: Results/Core_Features/G_6_core.qzv Saved FeatureTable[Frequency] to: Data/tables/J_2_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/J_2_7-lev_table.qza Saved Visualization to: Results/Core_Features/J_2_7-lev_core.qzv Saved Visualization to: Results/Core_Features/J_2_core.qzv Saved FeatureTable[Frequency] to: Data/tables/J_3_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/J_3_7-lev_table.qza Saved Visualization to: Results/Core_Features/J_3_7-lev_core.qzv Saved Visualization to: Results/Core_Features/J_3_core.qzv Saved FeatureTable[Frequency] to: Data/tables/J_4_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/J_4_7-lev_table.qza Saved Visualization to: Results/Core_Features/J_4_7-lev_core.qzv Saved Visualization to: Results/Core_Features/J_4_core.qzv Saved FeatureTable[Frequency] to: Data/tables/J_6_table.qza mkdir: missing operand Try 'mkdir --help' for more information. Saved FeatureTable[Frequency] to: Data/tables/J_6_7-lev_table.qza Saved Visualization to: Results/Core_Features/J_6_7-lev_core.qzv Saved Visualization to: Results/Core_Features/J_6_core.qzv
# By Niches and TimePoints separately
import pandas as pd
outdir= 'Results/Core_Features'
groups = ['S_2','S_3','S_4','S_6',
'R_2','R_3','R_4','R_6',
'G_2','G_3','G_4','G_6',
'J_2','J_3','J_4','J_6']
for group in groups:
temp = 'Data/Core_%s_temp' % group
coreqzv = 'Results/Core_Features/%s_core.qzv' % group
!mkdir $temp
!qiime tools export \
--input-path $coreqzv \
--output-path $temp
temp_7 = 'Data/Core_%s_temp_7' % group
core_7 = 'Results/Core_Features/%s_7-lev_core.qzv' % group
!mkdir $temp_7
!qiime tools export \
--input-path $core_7 \
--output-path $temp_7
Root, Gall, Soil, J2 = pd.DataFrame(), pd.DataFrame(), pd.DataFrame(), pd.DataFrame()
for group in groups:
temp = 'Data/Core_%s_temp' % group
core_tsv= temp+'/core-features-1.000.tsv'
core_pd = pd.read_csv(core_tsv, sep='\t')
core_pd = core_pd.filter(['Feature ID'], axis = 1)
core_pd.columns = [group]
if 'S' in group: Soil = pd.concat([Soil, core_pd], axis = 1)
if 'R' in group: Root = pd.concat([Root, core_pd], axis = 1)
if 'G' in group: Gall = pd.concat([Gall, core_pd], axis = 1)
if 'J' in group: J2 = pd.concat([J2, core_pd], axis = 1)
!rm -r $temp
Soil.to_csv('Results/Core_Features/Soil_tp.tsv', sep='\t')
Root.to_csv('Results/Core_Features/Root_tp.tsv', sep='\t')
Gall.to_csv('Results/Core_Features/Gall_tp.tsv', sep='\t')
J2.to_csv('Results/Core_Features/J2_tp.tsv', sep='\t')
Root, Gall, Soil, J2 = pd.DataFrame(), pd.DataFrame(), pd.DataFrame(), pd.DataFrame()
for group in groups:
temp_7 = 'Data/Core_%s_temp_7' % group
core_tsv= temp_7+'/core-features-1.000.tsv'
core_pd = pd.read_csv(core_tsv, sep='\t')
core_pd = core_pd.filter(['Feature ID'], axis = 1)
core_pd.columns = [group]
if 'S' in group: Soil = pd.concat([Soil, core_pd], axis = 1)
if 'R' in group: Root = pd.concat([Root, core_pd], axis = 1)
if 'G' in group: Gall = pd.concat([Gall, core_pd], axis = 1)
if 'J' in group: J2 = pd.concat([J2, core_pd], axis = 1)
!rm -r $temp_7
Soil.to_csv('Results/Core_Features/Soil_tp_lev-7.tsv', sep='\t')
Root.to_csv('Results/Core_Features/Root_tp_lev-7.tsv', sep='\t')
Gall.to_csv('Results/Core_Features/Gall_tp_lev-7.tsv', sep='\t')
J2.to_csv('Results/Core_Features/J2_tp_lev-7.tsv', sep='\t')
# Differences
import itertools
timepoints = [2,3,4,6]
variants = ['Infected', 'Root-Gall']
for variant in variants:
core_dt = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant
core_rs = 'Results/Longitudinal/%s' % variant
tabin = 'Data/tables/%s_table.qza' % variant
!mkdir -p $core_dt $core_rs/Pairwise-differences
for state, state_2 in itertools.combinations(timepoints, 2):
alpha_diversity = ['shannon', 'faith_pd', 'evenness', 'observed_otus']
for alpha in alpha_diversity:
vector=core_dt+'/%s_vector.qza' % alpha
param =core_rs+'/Pairwise-differences/%s_%s_pairwise-differences_parametric_%s-%s.qzv' %(variant,alpha,state,state_2)
no_par=core_rs+'/Pairwise-differences/%s_%s_pairwise-differences_no-parametric_%s-%s.qzv'%(variant,alpha,state,state_2)
if alpha == 'evenness':
metric = 'pielou_e'
else:
metric = alpha
!qiime longitudinal pairwise-differences \
--m-metadata-file Metadata/metadata.tsv \
--m-metadata-file $vector \
--p-metric $metric \
--p-group-column Niche \
--p-state-column TimePoint \
--p-state-1 $state \
--p-state-2 $state_2 \
--p-individual-id-column Location \
--p-replicate-handling random \
--p-no-parametric \
--o-visualization $no_par
!qiime longitudinal pairwise-differences \
--m-metadata-file Metadata/metadata.tsv \
--m-metadata-file $vector \
--p-metric $metric \
--p-group-column Niche \
--p-state-column TimePoint \
--p-state-1 $state \
--p-state-2 $state_2 \
--p-individual-id-column Location \
--p-replicate-handling random \
--p-parametric \
--o-visualization $param
Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_shannon_pairwise-differences_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_faith_pd_pairwise-differences_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_evenness_pairwise-differences_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-differences/Infected_observed_otus_pairwise-differences_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_shannon_pairwise-differences_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_faith_pd_pairwise-differences_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_evenness_pairwise-differences_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-differences/Root-Gall_observed_otus_pairwise-differences_parametric_4-6.qzv
#Distances
import itertools
timepoints = [2,3,4,6]
variants = ['Infected', 'Root-Gall']
for variant in variants:
core_dt = 'Data/Core-metrics_analysis/%s_Core-metrics' % variant
core_rs = 'Results/Longitudinal/%s' % variant
tabin = 'Data/tables/%s_table.qza' % variant
!mkdir $core_rs/Pairwise-distances
beta_diversity = ['unweighted_unifrac', 'weighted_unifrac', 'jaccard', 'bray_curtis']
for beta in beta_diversity:
for state, state_2 in itertools.combinations(timepoints, 2):
distance= core_dt+'/%s_distance_matrix.qza' % beta
output = core_rs+'/Pairwise-distances/%s_%s_pairwise-distances_no-parametric_%s-%s.qzv' % (variant, beta, state, state_2)
param = core_rs+'/Pairwise-distances/%s_%s_pairwise-distances_parametric_%s-%s.qzv' % (variant, beta, state, state_2)
!qiime longitudinal pairwise-distances \
--i-distance-matrix $distance \
--m-metadata-file Metadata/metadata.tsv \
--p-group-column Niche \
--p-state-column TimePoint \
--p-state-1 $state \
--p-state-2 $state_2 \
--p-individual-id-column Location \
--p-replicate-handling random \
--o-visualization $output
!qiime longitudinal pairwise-distances \
--i-distance-matrix $distance \
--m-metadata-file Metadata/metadata.tsv \
--p-group-column Niche \
--p-state-column TimePoint \
--p-state-1 $state \
--p-state-2 $state_2 \
--p-individual-id-column Location \
--p-replicate-handling random \
--p-parametric \
--o-visualization $param
mkdir: cannot create directory ‘Results/Longitudinal/Infected/Pairwise-distances’: File exists Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_unweighted_unifrac_pairwise-distances_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_weighted_unifrac_pairwise-distances_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_jaccard_pairwise-distances_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Infected/Pairwise-distances/Infected_bray_curtis_pairwise-distances_parametric_4-6.qzv mkdir: cannot create directory ‘Results/Longitudinal/Root-Gall/Pairwise-distances’: File exists Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_unweighted_unifrac_pairwise-distances_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_weighted_unifrac_pairwise-distances_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_jaccard_pairwise-distances_parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_no-parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_parametric_2-3.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_no-parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_parametric_2-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_no-parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_parametric_2-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_no-parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_parametric_3-4.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_no-parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_parametric_3-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_no-parametric_4-6.qzv Saved Visualization to: Results/Longitudinal/Root-Gall/Pairwise-distances/Root-Gall_bray_curtis_pairwise-distances_parametric_4-6.qzv
#By_Niches
niches = ['Gall','Root','J2','Soil']
levels = ['Taxa','ASV']
for level in levels:
for niche in niches:
out_rs = 'Results/Longitudinal/By_Niches/%s_%s_Feature_Volatility' %(niche,level)
out_dt = 'Data/Longitudinal/By_Niches/%s_%s_Feature_Volatility' %(niche,level)
volplot= out_rs + '/%s_%s_volatility-plot.qzv' %(niche,level)
tabin = 'Data/tables/%s_table.qza' %niche
tabin7 = 'Data/tables/%s_table_7_all_tp.qza' %niche
if level == 'Taxa':
table = tabin7
!qiime taxa collapse \
--i-table $tabin \
--i-taxonomy Data/combo_taxonomy.qza \
--p-level 7 \
--o-collapsed-table $tabin7
else:
table = tabin
!mkdir -p $out_rs
!qiime longitudinal feature-volatility \
--i-table $table \
--m-metadata-file Metadata/metadata.tsv \
--p-state-column TimePoint \
--p-individual-id-column Location \
--output-dir $out_dt \
--p-n-jobs 16 \
--p-feature-count 'all' \
--o-volatility-plot $volplot
#!rm Data/Longitudinal/By_Niches
Saved FeatureTable[Frequency] to: Data/tables/Gall_table_7_all_tp.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/Gall_Taxa_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/Gall_Taxa_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/Gall_Taxa_Feature_Volatility/Gall_Taxa_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/Gall_Taxa_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/Gall_Taxa_Feature_Volatility/sample_estimator.qza Saved FeatureTable[Frequency] to: Data/tables/Root_table_7_all_tp.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/Root_Taxa_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/Root_Taxa_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/Root_Taxa_Feature_Volatility/Root_Taxa_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/Root_Taxa_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/Root_Taxa_Feature_Volatility/sample_estimator.qza Saved FeatureTable[Frequency] to: Data/tables/J2_table_7_all_tp.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/J2_Taxa_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/J2_Taxa_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/J2_Taxa_Feature_Volatility/J2_Taxa_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/J2_Taxa_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/J2_Taxa_Feature_Volatility/sample_estimator.qza Saved FeatureTable[Frequency] to: Data/tables/Soil_table_7_all_tp.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/Soil_Taxa_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/Soil_Taxa_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/Soil_Taxa_Feature_Volatility/Soil_Taxa_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/Soil_Taxa_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/Soil_Taxa_Feature_Volatility/sample_estimator.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/Gall_ASV_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/Gall_ASV_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/Gall_ASV_Feature_Volatility/Gall_ASV_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/Gall_ASV_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/Gall_ASV_Feature_Volatility/sample_estimator.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/Root_ASV_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/Root_ASV_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/Root_ASV_Feature_Volatility/Root_ASV_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/Root_ASV_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/Root_ASV_Feature_Volatility/sample_estimator.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/J2_ASV_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/J2_ASV_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/J2_ASV_Feature_Volatility/J2_ASV_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/J2_ASV_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/J2_ASV_Feature_Volatility/sample_estimator.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/By_Niches/Soil_ASV_Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/By_Niches/Soil_ASV_Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/By_Niches/Soil_ASV_Feature_Volatility/Soil_ASV_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/By_Niches/Soil_ASV_Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/By_Niches/Soil_ASV_Feature_Volatility/sample_estimator.qza rm: cannot remove 'Data/Longitudinal/By_Niches': Is a directory
variants = ['Infected', 'Root-Gall']
for variant in variants:
tabin = 'Data/tables/%s_table.qza' % variant
out_rs = 'Results/Longitudinal/%s/Feature_Volatility' % variant
out_dt = 'Data/Longitudinal/%s/Feature_Volatility' % variant
volplot= out_rs + '/%s_volatility-plot.qzv' % variant
!mkdir -p $out_rs
!qiime longitudinal feature-volatility \
--i-table $tabin \
--m-metadata-file Metadata/metadata.tsv \
--p-state-column TimePoint \
--p-individual-id-column Location \
--output-dir $out_dt \
--p-n-jobs 16 \
--p-feature-count 'all' \
--o-volatility-plot $volplot
out_rs_level = 'Results/Longitudinal/%s/Feature_Volatility_lev-7' % variant
out_dt_level = 'Data/Longitudinal/%s/Feature_Volatility_lev-7' % variant
tabout_level = 'Data/Longitudinal/%s_7_table.qza' % variant
volplot_level= out_rs_level + '/%s_volatility-plot_7-lev.qzv' % variant
!mkdir -p $out_rs_level
!qiime taxa collapse \
--i-table $tabin \
--i-taxonomy Data/combo_taxonomy.qza \
--p-level 7 \
--o-collapsed-table $tabout_level
!qiime longitudinal feature-volatility \
--i-table $tabout_level \
--m-metadata-file Metadata/metadata.tsv \
--p-state-column TimePoint \
--p-individual-id-column Location \
--p-n-jobs 16 \
--p-feature-count 'all' \
--output-dir $out_dt_level \
--o-volatility-plot $volplot_level
#!rm Data/Longitudinal
Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/Infected/Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/Infected/Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/Infected/Feature_Volatility/Infected_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/Infected/Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/Infected/Feature_Volatility/sample_estimator.qza Saved FeatureTable[Frequency] to: Data/Longitudinal/Infected_7_table.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/Infected/Feature_Volatility_lev-7/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/Infected/Feature_Volatility_lev-7/feature_importance.qza Saved Visualization to: Results/Longitudinal/Infected/Feature_Volatility_lev-7/Infected_volatility-plot_7-lev.qzv Saved Visualization to: Data/Longitudinal/Infected/Feature_Volatility_lev-7/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/Infected/Feature_Volatility_lev-7/sample_estimator.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/Root-Gall/Feature_Volatility/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/Root-Gall/Feature_Volatility/feature_importance.qza Saved Visualization to: Results/Longitudinal/Root-Gall/Feature_Volatility/Root-Gall_volatility-plot.qzv Saved Visualization to: Data/Longitudinal/Root-Gall/Feature_Volatility/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/Root-Gall/Feature_Volatility/sample_estimator.qza Saved FeatureTable[Frequency] to: Data/Longitudinal/Root-Gall_7_table.qza Saved FeatureTable[RelativeFrequency] to: Data/Longitudinal/Root-Gall/Feature_Volatility_lev-7/filtered_table.qza Saved FeatureData[Importance] to: Data/Longitudinal/Root-Gall/Feature_Volatility_lev-7/feature_importance.qza Saved Visualization to: Results/Longitudinal/Root-Gall/Feature_Volatility_lev-7/Root-Gall_volatility-plot_7-lev.qzv Saved Visualization to: Data/Longitudinal/Root-Gall/Feature_Volatility_lev-7/accuracy_results.qzv Saved SampleEstimator[Regressor] to: Data/Longitudinal/Root-Gall/Feature_Volatility_lev-7/sample_estimator.qza
!mkdir Data/97_OTU
!qiime vsearch cluster-features-de-novo \
--i-table Data/tables/table.qza \
--i-sequences Data/rep-seqs.qza \
--p-perc-identity 0.97 \
--o-clustered-table Data/97_OTU/table_97-OTU.qza \
--o-clustered-sequences Data/97_OTU/rep-seqs_97.qza
!qiime feature-table summarize \
--i-table Data/97_OTU/table_97-OTU.qza \
--o-visualization Data/97_OTU/table_97-OTU.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
mkdir: cannot create directory ‘Data/97_OTU’: File exists Saved FeatureTable[Frequency] to: Data/97_OTU/table_97-OTU.qza Saved FeatureData[Sequence] to: Data/97_OTU/rep-seqs_97.qza Saved Visualization to: Data/97_OTU/table_97-OTU.qzv
!qiime feature-table filter-features \
--i-table Data/97_OTU/table_97-OTU.qza \
--p-min-frequency 10 \
--p-min-samples 5 \
--o-filtered-table Data/97_OTU/filtered-table.qza
!qiime taxa filter-table \
--i-table Data/97_OTU/filtered-table.qza \
--i-taxonomy Data/taxonomy.qza \
--p-exclude mitochondria,chloroplast \
--o-filtered-table Data/97_OTU/filtered-table.qza
!qiime feature-table filter-samples \
--i-table Data/97_OTU/filtered-table.qza \
--p-min-features 25 \
--p-min-frequency 8000 \
--o-filtered-table Data/97_OTU/filtered-table.qza
!qiime feature-table filter-samples \
--i-table Data/97_OTU/filtered-table.qza \
--m-metadata-file Data/tables/samples_to_exclude.tsv \
--p-exclude-ids \
--o-filtered-table Data/97_OTU/filtered-table.qza
!qiime feature-table summarize \
--i-table Data/97_OTU/filtered-table.qza \
--o-visualization Data/97_OTU/filtered-table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
!qiime taxa filter-table \
--i-table Data/97_OTU/filtered-table.qza \
--i-taxonomy Data/taxonomy.qza \
--p-include D_1__ \
--o-filtered-table Data/97_OTU/filtered-table.qza
!qiime feature-table summarize \
--i-table Data/97_OTU/filtered-table.qza \
--o-visualization Data/97_OTU/filtered-table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
Saved FeatureTable[Frequency] to: Data/97_OTU/filtered-table.qza Saved FeatureTable[Frequency] to: Data/97_OTU/filtered-table.qza Saved FeatureTable[Frequency] to: Data/97_OTU/filtered-table.qza Saved FeatureTable[Frequency] to: Data/97_OTU/filtered-table.qza Saved Visualization to: Data/97_OTU/filtered-table.qzv Saved FeatureTable[Frequency] to: Data/97_OTU/filtered-table.qza Saved Visualization to: Data/97_OTU/filtered-table.qzv
!qiime feature-table filter-samples \
--i-table Data/97_OTU/filtered-table.qza \
--m-metadata-file Metadata/metadata.tsv \
--p-where "Treatment='Infected'" \
--o-filtered-table Data/97_OTU/Infected_table.qza
!qiime feature-table summarize \
--i-table Data/97_OTU/Infected_table.qza \
--o-visualization Data/97_OTU/Infected_table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
!qiime feature-table filter-samples \
--i-table Data/97_OTU/Infected_table.qza \
--m-metadata-file Metadata/metadata.tsv \
--p-where "Niche IN ('Root','Gall')" \
--o-filtered-table Data/97_OTU/Root-Gall_table.qza
!qiime feature-table summarize \
--i-table Data/97_OTU/Root-Gall_table.qza \
--o-visualization Data/97_OTU/Root-Gall_table.qzv \
--m-sample-metadata-file Metadata/metadata.tsv
Saved FeatureTable[Frequency] to: Data/97_OTU/Infected_table.qza Saved Visualization to: Data/97_OTU/Infected_table.qzv Saved FeatureTable[Frequency] to: Data/97_OTU/Root-Gall_table.qza Saved Visualization to: Data/97_OTU/Root-Gall_table.qzv
!qiime phylogeny align-to-tree-mafft-fasttree \
--i-sequences Data/97_OTU/rep-seqs_97.qza \
--o-alignment Data/97_OTU/aligned-rep-seqs.qza \
--o-masked-alignment Data/97_OTU/masked-aligned-rep-seqs.qza \
--o-tree Data/97_OTU/unrooted-tree.qza \
--o-rooted-tree Data/97_OTU/rooted-tree_97-OTU.qza \
--p-n-threads 4
Saved FeatureData[AlignedSequence] to: Data/97_OTU/aligned-rep-seqs.qza Saved FeatureData[AlignedSequence] to: Data/97_OTU/masked-aligned-rep-seqs.qza Saved Phylogeny[Unrooted] to: Data/97_OTU/unrooted-tree.qza Saved Phylogeny[Rooted] to: Data/97_OTU/rooted-tree_97-OTU.qza
!mkdir Results/Core-metrics_analysis_97-OTU
variants = ['Root-Gall', 'Infected']
for variant in variants:
Rslt_core = 'Results/Core-metrics_analysis_97-OTU/%s_Core-metrics' % variant
tabin = 'Data/97_OTU/%s_table.qza' % variant
!qiime diversity core-metrics-phylogenetic \
--i-phylogeny Data/97_OTU/rooted-tree_97-OTU.qza \
--i-table $tabin \
--p-sampling-depth 8867 \
--m-metadata-file Metadata/metadata.tsv \
--p-n-jobs 4 \
--output-dir $Rslt_core
Saved FeatureTable[Frequency] to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/rarefied_table.qza Saved SampleData[AlphaDiversity] % Properties('phylogenetic') to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/faith_pd_vector.qza Saved SampleData[AlphaDiversity] to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/observed_otus_vector.qza Saved SampleData[AlphaDiversity] to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/shannon_vector.qza Saved SampleData[AlphaDiversity] to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/evenness_vector.qza Saved DistanceMatrix % Properties('phylogenetic') to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/unweighted_unifrac_distance_matrix.qza Saved DistanceMatrix % Properties('phylogenetic') to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/weighted_unifrac_distance_matrix.qza Saved DistanceMatrix to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/jaccard_distance_matrix.qza Saved DistanceMatrix to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/bray_curtis_distance_matrix.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/unweighted_unifrac_pcoa_results.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/weighted_unifrac_pcoa_results.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/jaccard_pcoa_results.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/bray_curtis_pcoa_results.qza Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/unweighted_unifrac_emperor.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/weighted_unifrac_emperor.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/jaccard_emperor.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/bray_curtis_emperor.qzv Saved FeatureTable[Frequency] to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/rarefied_table.qza Saved SampleData[AlphaDiversity] % Properties('phylogenetic') to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/faith_pd_vector.qza Saved SampleData[AlphaDiversity] to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/observed_otus_vector.qza Saved SampleData[AlphaDiversity] to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/shannon_vector.qza Saved SampleData[AlphaDiversity] to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/evenness_vector.qza Saved DistanceMatrix % Properties('phylogenetic') to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/unweighted_unifrac_distance_matrix.qza Saved DistanceMatrix % Properties('phylogenetic') to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/weighted_unifrac_distance_matrix.qza Saved DistanceMatrix to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/jaccard_distance_matrix.qza Saved DistanceMatrix to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/bray_curtis_distance_matrix.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/unweighted_unifrac_pcoa_results.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/weighted_unifrac_pcoa_results.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/jaccard_pcoa_results.qza Saved PCoAResults to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/bray_curtis_pcoa_results.qza Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/unweighted_unifrac_emperor.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/weighted_unifrac_emperor.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/jaccard_emperor.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/bray_curtis_emperor.qzv
variants = ['Root-Gall', 'Infected']
for variant in variants:
core = 'Results/Core-metrics_analysis_97-OTU/%s_Core-metrics' % variant
#Alpha diversity comparisons¶
alpha_diversity = ['shannon', 'faith_pd', 'evenness', 'observed_otus']
for alpha in alpha_diversity:
vector = core+'/%s_vector.qza' % alpha
ags_qzv = core+'/%s_vector_alpha-group-sign.qzv' % alpha
!qiime diversity alpha-group-significance \
--i-alpha-diversity $vector \
--m-metadata-file Metadata/metadata.tsv \
--o-visualization $ags_qzv
Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/shannon_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/faith_pd_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/evenness_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Root-Gall_Core-metrics/observed_otus_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/shannon_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/faith_pd_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/evenness_vector_alpha-group-sign.qzv Saved Visualization to: Results/Core-metrics_analysis_97-OTU/Infected_Core-metrics/observed_otus_vector_alpha-group-sign.qzv