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

# ### Running in Docker container on Swoose
# 
# Started Docker container with the following command:
# 
# ```docker run -p 8888:8888 -v /home/sam/data/:/home/data -it bioinformatics/bioinformatics:v0 /bin/bash```
# 
# The command allows /home/sam/data/ to be accessible to the Docker container.
# Once access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files the container was started, started Jupyter Notebook with the following command inside the Docker container:
# 
# ```jupyter notebook --allow-root```
# 
# This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888. The Docker container is running on an image created from this Dockerfile (Git commit [ece177e](https://github.com/RobertsLab/code/commit/ece177e2ad73b5eff5daa67d9000e198a704ff1d))

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get_ipython().run_cell_magic('bash', '', 'date\n')


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get_ipython().run_cell_magic('bash', '', 'lscpu\n')


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get_ipython().run_cell_magic('bash', '', 'free -mh\n')


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get_ipython().run_cell_magic('bash', '', 'pwd\n')


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get_ipython().run_cell_magic('bash', '', 'mkdir /home/data/20171005_redundans\n')


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cd 20171005_redundans/


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get_ipython().run_cell_magic('bash', '', 'cd ..\nrmdir 20171005_redundans\n')


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get_ipython().run_cell_magic('bash', '', 'cd\n')


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get_ipython().run_cell_magic('bash', '', 'date\n')


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get_ipython().run_cell_magic('bash', '', 'pwd\n')


# ### Redundans using Racon assembly as FASTA reference
# 
# #### PacBio reads (m17 files) and Illumina files (151 and 160 files)

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get_ipython().system('python /usr/local/bioinformatics/redundans/redundans.py  -t 24  -l  m170211_224036_42134_c101073082550000001823236402101737_s1_X0_filtered_subreads.fastq.gz  m170301_100013_42134_c101174162550000001823269408211761_s1_p0_filtered_subreads.fastq.gz  m170301_162825_42134_c101174162550000001823269408211762_s1_p0_filtered_subreads.fastq.gz  m170301_225711_42134_c101174162550000001823269408211763_s1_p0_filtered_subreads.fastq.gz  m170308_163922_42134_c101174252550000001823269408211742_s1_p0_filtered_subreads.fastq.gz  m170308_230815_42134_c101174252550000001823269408211743_s1_p0_filtered_subreads.fastq.gz  m170315_001112_42134_c101169372550000001823273008151717_s1_p0_filtered_subreads.fastq.gz  m170315_063041_42134_c101169382550000001823273008151700_s1_p0_filtered_subreads.fastq.gz  m170315_124938_42134_c101169382550000001823273008151701_s1_p0_filtered_subreads.fastq.gz  m170315_190851_42134_c101169382550000001823273008151702_s1_p0_filtered_subreads.fastq.gz  -i  151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.gz  151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.gz  151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.gz  151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.gz  151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.gz  151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.gz  160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.gz  160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.gz  160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.gz  160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.gz  160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.gz  160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.gz  160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.gz  160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.gz  160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.gz  160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz  160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.gz  160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.gz  -f  /home/data/pacbio_oly/20170918_oly_pacbio_racon1_consensus.fasta  -o  /home/data/20171005_redundans/')


# ### Run QUAST to compare Redundans with Canu (Sean's PacBio assembly) and Racon (my PacBio assembly)

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get_ipython().system('python /usr/local/bioinformatics/quast-4.5/quast.py  -t 24  /home/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa  /home/data/20171005_redundans/scaffolds.reduced.fa')


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get_ipython().run_cell_magic('bash', '', 'cat quast_results/results_2017_10_06_22_21_06/report.txt\n')


# #### Run QUAST using --scaffolds option

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get_ipython().system('python /usr/local/bioinformatics/quast-4.5/quast.py --scaffolds  -t 24  /home/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa  /home/data/20171005_redundans/scaffolds.reduced.fa')


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get_ipython().run_cell_magic('bash', '', 'cat quast_results/results_2017_10_06_22_27_26/report.txt\n')


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get_ipython().run_cell_magic('bash', '', 'cp -r quast_results/results_2017_10_06_22_21_06/ /home/owl/Athaliana/quast_results/\n')


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


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get_ipython().run_cell_magic('bash', '', 'cp -r quast_results/results_2017_10_06_22_27_26/ /home/owl/Athaliana/quast_results/\n')


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


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get_ipython().run_cell_magic('html', '', 'http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_06_22_21_06/report.html\n')


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get_ipython().run_cell_magic('html', '', 'http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_06_22_27_26/report.html\n')


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get_ipython().run_cell_magic('bash', '', 'cp -r 20171005_redundans/ /home/owl/Athaliana/\n')


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get_ipython().run_cell_magic('bash', '', 'ls /home/owl/Athaliana/20171005_redundans/\n')


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