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

# ### Running in Docker container on Ostrich
# 
# #### Started Docker container with the following command:
# 
# ```docker run -p 8888:8888 -v /Users/sam/data/:/data -v /Users/sam/owl_home/:/owl_home -v /Users/sam/owl_web/:/owl_web -v /Users/sam/gitrepos:/gitrepos -it f99537d7e06a```
# 
# The command allows access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files on Owl/home and Owl/web accessible to the Docker container.
# 
# Once the container was started, started Jupyter Notebook with the following command inside the Docker container:
# 
# ```jupyter notebook```
# 
# 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 443bc42)](https://github.com/sr320/LabDocs/blob/443bc425cd36d23a07cf12625f38b7e3a397b9be/code/dockerfiles/Dockerfile.bio)

# In[1]:


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


# ### Check computer specs

# In[2]:


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


# In[3]:


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


# In[4]:


cd /gitrepos/Reseqtools/iTools_Code/


# ### Double check files before beginning

# Check for raw FASTQ files

# In[5]:


ls /data/oly_gbs_raw/


# Verify index file looks OK.

# In[6]:


get_ipython().run_cell_magic('bash', '', 'head /data/oly_gbs_raw/index.lst\n')


# Whoops! That's not right! I forgot I moved the corrected files to my paper repo...

# In[7]:


ls /gitrepos/paper_oly_gbs/data/


# In[8]:


get_ipython().run_cell_magic('bash', '', 'head /gitrepos/paper_oly_gbs/data/index.lst\nhead /gitrepos/paper_oly_gbs/data/enzyme.txt\n')


# Looks good!

# ### Run BGI demultiplexing script

# In[9]:


get_ipython().run_cell_magic('bash', '', 'time ./iTools Fqtools splitpool \\\n-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \\\n-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \\\n-Index /gitrepos/paper_oly_gbs/data/index.lst \\\n-Flag /gitrepos/paper_oly_gbs/dataenzyme.txt \\\n-MisMatch \\\n-OutDir /data/oly_gbs_raw/split/\n')


# Ugh. Ran it to the same directory as I did the last time I ran the script! Need to change to a different directory... 
# 
# This also means that some of the files from the first run are probably screwed up!
# 
# However, the goal of this is to compare a subset of the output and see if the two runs produced different results. Don't need all the files in order to do that comparison.

# In[10]:


get_ipython().run_cell_magic('bash', '', 'time ./iTools Fqtools splitpool \\\n-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \\\n-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \\\n-Index /gitrepos/paper_oly_gbs/data/index.lst \\\n-Flag /gitrepos/paper_oly_gbs/dataenzyme.txt \\\n-MisMatch \\\n-OutDir /data/oly_gbs_raw/split2/\n')


# In[ ]:


get_ipython().run_cell_magic('bash', '', 'ls -lh /data/oly_gbs_raw/split/ | head\n')


# Nope. I screwed it up. The demultplexing I ran in Step 9 overwrote everything from the first run!
# 
# Well, let's run it again so we have files to compare...

# In[ ]:


get_ipython().run_cell_magic('bash', '', 'time ./iTools Fqtools splitpool \\\n-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \\\n-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \\\n-Index /gitrepos/paper_oly_gbs/data/index.lst \\\n-Flag /gitrepos/paper_oly_gbs/dataenzyme.txt \\\n-MisMatch \\\n-OutDir /data/oly_gbs_raw/split/\n')


# Arrived to lab this morning to disconnects errors. Let's see if these worked...

# In[1]:


get_ipython().run_cell_magic('bash', '', 'ls -lh /data/oly_gbs_raw/split/ | head\n')


# In[2]:


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


# In[3]:


get_ipython().run_cell_magic('bash', '', 'ls -lh /data/oly_gbs_raw/split2/\n')


# OMG! There's a typo in the both of the demultiplexing scripts above! The path to the enzyme list is incorrect... :( Let's run them again...
# 
# It certainly would be nice if some checks were built into this program (and, it's be nice if I was paying more attention)!

# In[4]:


get_ipython().run_cell_magic('bash', '', 'time ./iTools Fqtools splitpool \\\n-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \\\n-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \\\n-Index /gitrepos/paper_oly_gbs/data/index.lst \\\n-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \\\n-MisMatch \\\n-OutDir /data/oly_gbs_raw/split2/\n')


# In[5]:


get_ipython().run_cell_magic('bash', '', 'time ./iTools Fqtools splitpool \\\n-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \\\n-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \\\n-Index /gitrepos/paper_oly_gbs/data/index.lst \\\n-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \\\n-MisMatch \\\n-OutDir /data/oly_gbs_raw/split/\n')


# In[6]:


cd /gitrepos/Reseqtools/iTools_Code/


# In[7]:


get_ipython().run_cell_magic('bash', '', 'time ./iTools Fqtools splitpool \\\n-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \\\n-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \\\n-Index /gitrepos/paper_oly_gbs/data/index.lst \\\n-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \\\n-MisMatch \\\n-OutDir /data/oly_gbs_raw/split/\n')


# In[8]:


get_ipython().run_cell_magic('bash', '', 'time ./iTools Fqtools splitpool \\\n-InFq1 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz \\\n-InFq2 /data/oly_gbs_raw/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz \\\n-Index /gitrepos/paper_oly_gbs/data/index.lst \\\n-Flag /gitrepos/paper_oly_gbs/data/enzyme.txt \\\n-MisMatch \\\n-OutDir /data/oly_gbs_raw/split2/\n')


# In[ ]: