#!/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))

# In[1]:


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


# In[2]:


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


# In[3]:


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


# In[4]:


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


# In[5]:


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


# #### Print list of files for easy copying/pasting into redundans command

# In[6]:


get_ipython().run_cell_magic('bash', '', 'for i in /home/data/*subreads*\ndo\necho "$i"\ndone\n')


# #### Print list of PacBio files for easy copying/pasting into redundans command

# In[7]:


get_ipython().run_cell_magic('bash', '', 'cd ..\nfor i in *subreads*\ndo\necho "$i"\ndone\n')


# In[8]:


get_ipython().run_cell_magic('bash', '', 'for i in 1[56]*\ndo\necho "$i"\ndone\n')


# In[9]:


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


# #### Print list of Illumina files for easy copying/pasting into redundans command

# In[10]:


get_ipython().run_cell_magic('bash', '', 'cd ..\nfor i in 1[56]*\ndo\necho "$i"\ndone\n')


# In[11]:


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  -o  /home/data/20171003_redundans/')


# #### This isn't the cause of the error message above, but just realized I'm in the wrong directory.

# In[12]:


cd ..


# In[13]:


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  oly_pacbio_.contigs.fasta  -o  /home/data/20171003_redundans/')


# #### Ah, I see the error now! Need to remove space between hyphen and "f" option!

# In[14]:


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  oly_pacbio_.contigs.fasta  -o  /home/data/20171003_redundans/')


# ### Run redundans
# 
# #### The FASTA file used below is an assembly generated by [Sean with Canu](http://owl.fish.washington.edu/scaphapoda/Sean/Oly_Canu_Output/)

# In[15]:


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  oly_pacbio_.contigs.fasta  -o  /home/data/20171003_redundans_01/')


# ### Compare to Sean's redundans runs

# #### Set file locations as variables

# In[16]:


sb_redundans1="/home/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa"
sb_redundans2="/home/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa"
sjw_reduandans="/home/data/20171003_redundans_01/scaffolds.reduced.fa"


# #### Run QUAST to assess assemblies
# 
# ##### First, I'll run without --scaffolds option.

# In[17]:


get_ipython().system('python /usr/local/bioinformatics/quast-4.5/quast.py  -t 24  $sb_redundans1  $sb_redundans2  $sjw_reduandans')


# In[18]:


get_ipython().run_cell_magic('bash', '', 'cat quast_results/results_2017_10_05_14_21_50/report.txt\n')


# #### Run with --scaffolds option

# In[19]:


get_ipython().system('python /usr/local/bioinformatics/quast-4.5/quast.py --scaffolds -t 24  $sb_redundans1  $sb_redundans2  $sjw_reduandans')


# In[20]:


get_ipython().system('python /usr/local/bioinformatics/quast-4.5/quast.py --scaffolds  -t 24  $sb_redundans1  $sb_redundans2  $sjw_reduandans')


# In[21]:


get_ipython().run_cell_magic('bash', '', 'cat quast_results/results_2017_10_05_14_28_51/report.txt\n')


# In[22]:


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


# In[23]:


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


# In[24]:


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


# In[25]:


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


# In[26]:


get_ipython().run_cell_magic('bash', '', 'cp -r quast_results/results_2017_10_05_14_21_50/ /home/owl/Athaliana/quast_results/\n')


# In[27]:


get_ipython().run_cell_magic('bash', '', 'cp -r quast_results/results_2017_10_05_14_28_51/ /home/owl/Athaliana/quast_results/\n')


# In[28]:


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


# In[29]:


get_ipython().run_cell_magic('bash', '', 'rm -rf /home/owl/Athaliana/quast_results/\n')


# In[30]:


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


# In[31]:


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


# ### Results of first Quast run (i.e. without --scaffolds option)

# In[32]:


get_ipython().run_cell_magic('html', '', 'http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_05_14_21_50/report.html\n')


# ### Results of second Quast run (i.e. using --scaffolds option)

# In[33]:


get_ipython().run_cell_magic('html', '', 'http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_10_05_14_28_51/report.html\n')


# In[34]:


cp -r /home/data/20171003_redundans_01/ /home/owl/Athaliana/


# In[35]:


get_ipython().run_cell_magic('bash', '', 'ls /home/owl/Athaliana/20171003_redundans_01/\n')


# In[36]:


get_ipython().run_cell_magic('bash', '', 'mv /home/owl/Athaliana/20171003_redundans_01/ /home/owl/Athaliana/20171004_redundans/\n')


# In[ ]: