from os import chdir, mkdir
from os.path import join
# these are only available in the current development branch of IPython
from IPython.display import FileLinks, FileLink

!wget https://s3.amazonaws.com/s3-qiime_tutorial_files/moving_pictures_tutorial-1.8.0.tgz
!wget ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz
!tar -xzf moving_pictures_tutorial-1.8.0.tgz
!tar -xzf gg_13_8_otus.tar.gz

otu_base = "gg_13_8_otus/"
reference_seqs = join(otu_base,"rep_set/97_otus.fasta")
reference_tree = join(otu_base,"trees/97_otus.tree")
reference_tax = join(otu_base,"taxonomy/97_otu_taxonomy.txt")

!ls moving_pictures_tutorial-1.8.0

FileLinks('moving_pictures_tutorial-1.8.0')

!check_id_map.py -o moving_pictures_tutorial-1.8.0/illumina/cid_l1/ -m moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l1.txt

!split_libraries_fastq.py -o moving_pictures_tutorial-1.8.0/illumina/slout/ -i moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_1_sequence.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_2_sequence.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_3_sequence.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_4_sequence.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_5_sequence.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_6_sequence.fastq -b moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_1_sequence_barcodes.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_2_sequence_barcodes.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_3_sequence_barcodes.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_4_sequence_barcodes.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_5_sequence_barcodes.fastq,moving_pictures_tutorial-1.8.0/illumina/raw/subsampled_s_6_sequence_barcodes.fastq -m moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l1.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l2.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l3.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l4.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l5.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l6.txt

FileLinks('moving_pictures_tutorial-1.8.0/illumina/slout/')

!count_seqs.py -i moving_pictures_tutorial-1.8.0/illumina/slout/seqs.fna

!pick_open_reference_otus.py -o moving_pictures_tutorial-1.8.0/illumina/otus/ -i moving_pictures_tutorial-1.8.0/illumina/slout/seqs.fna -r $reference_seqs -p moving_pictures_tutorial-1.8.0/uc_fast_params.txt

FileLinks('moving_pictures_tutorial-1.8.0/illumina/otus/')

!biom summarize-table -i moving_pictures_tutorial-1.8.0/illumina/otus/otu_table_mc2_w_tax_no_pynast_failures.biom -o moving_pictures_tutorial-1.8.0/illumina/otus/otu_table_mc2_w_tax_no_pynast_failures_summary.txt

FileLink('moving_pictures_tutorial-1.8.0/illumina/otus/otu_table_mc2_w_tax_no_pynast_failures_summary.txt')

!merge_mapping_files.py -o moving_pictures_tutorial-1.8.0/illumina/combined_mapping_file.txt -m moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l1.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l2.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l3.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l4.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l5.txt,moving_pictures_tutorial-1.8.0/illumina/raw/filtered_mapping_l6.txt

FileLink('moving_pictures_tutorial-1.8.0/illumina/combined_mapping_file.txt')

!core_diversity_analyses.py -o moving_pictures_tutorial-1.8.0/illumina/otus/cd258/ --suppress_alpha_diversity -i moving_pictures_tutorial-1.8.0/illumina/otus/otu_table_mc2_w_tax_no_pynast_failures.biom -m moving_pictures_tutorial-1.8.0/illumina/combined_mapping_file.txt -t moving_pictures_tutorial-1.8.0/illumina/otus/rep_set.tre -e 258 -c "SampleType,days_since_epoch"

FileLink('moving_pictures_tutorial-1.8.0/illumina/otus/cd258/index.html')