#!/usr/bin/env python
# coding: utf-8

# In[1]:


get_ipython().run_cell_magic('bash', '', 'echo "TODAY\'S DATE"\ndate\necho "------------"\necho ""\nlsb_release -a\necho ""\necho "------------"\necho "HOSTNAME: "\nhostname\necho ""\necho "------------"\necho "Computer Specs:"\necho ""\nlscpu\necho ""\necho "------------"\necho ""\necho "Memory Specs"\necho ""\nfree -mh\n')


# ### Compare assemblies using [Quast v4.5](http://quast.sourceforge.net/quast)

# #### Set file locations as variables.

# In[2]:


canu_sb_01="/mnt/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta"
canu_sjw_01="/mnt/owl/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta"
pbjelly_sjw_01="/mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta"
platanus_sb_01="/mnt/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa"
platanus_sb_02="/mnt/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa"
racon_sjw_01="/mnt/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta"
redundans_sb_01="/mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa"
redundans_sb_02="/mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa"
redundans_sjw_01="/mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa"
redundans_sjw_02="/mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa"
redundans_sjw_03="/mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa"
soap_bgi_01="/mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa"


# In[3]:


get_ipython().system('python /home/sam/software/quast-4.5/quast.py  -t 24  $canu_sb_01  $canu_sjw_01  $pbjelly_sjw_01  $platanus_sb_01  $platanus_sb_02  $racon_sjw_01  $redundans_sb_01  $redundans_sb_02  $redundans_sjw_01  $redundans_sjw_02  $redundans_sjw_03  $soap_bgi_01')


# In[4]:


get_ipython().run_cell_magic('bash', '', 'cp -pR quast_results/results_2018_01_16_10_08_35/ /mnt/owl/Athaliana/quast_results/\n')


# #### Needed to use ```sudo``` to cp, so did that outside of notebook.

# In[5]:


get_ipython().run_cell_magic('bash', '', 'ls /mnt/owl/Athaliana/quast_results/results_2018_01_16_10_08_35/\n')


# OK, so this all worked. However, text file output is difficult to view in Jupyter notebook. View it here: [http://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/report.txt](http://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/report.txt)
# 
# Use this link to view color-coded table of output:
# 
# [http://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/report.html](http://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/report.html)

# In[ ]: