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

# In[1]:


get_ipython().run_cell_magic('bash', '', 'echo "TODAY\'S DATE:"\ndate\necho "------------"\necho ""\n#Display operating system info\nlsb_release -a\necho ""\necho "------------"\necho "HOSTNAME: "; hostname \necho ""\necho "------------"\necho "Computer Specs:"\necho ""\nlscpu\necho ""\necho "------------"\necho ""\necho "Memory Specs"\necho ""\nfree -mh\n')


# ### Download necessary files

# In[2]:


get_ipython().run_cell_magic('bash', '', 'mkdir /home/sam/data/Cvirginica\ncd /home/sam/data/Cvirginica\ntime \\\nwget \\\n--quiet \\\n--no-directories \\\n--recursive \\\n--accept gz \\\n--accept-regex "2112_lane1_[ATCG]"\nhttp://owl.fish.washington.edu/nightingales/C_virginica/\nsed \'/^Subject:/ s/ / virginica download JOB COMPLETE/\' ~/.default-subject.mail | msmtp "$EMAIL"\n\nls -ltrh\n')


# #### Fix typo - forgot line continuation slash after regex line.

# In[3]:


get_ipython().run_cell_magic('bash', '', 'cd /home/sam/data/Cvirginica\ntime \\\nwget \\\n--quiet \\\n--no-directories \\\n--recursive \\\n--accept gz \\\n--accept-regex "2112_lane1_[ATCG]" \\\nhttp://owl.fish.washington.edu/nightingales/C_virginica/\nsed \'/^Subject:/ s/ / virginica download JOB COMPLETE/\' ~/.default-subject.mail | msmtp "$EMAIL"\n\nls -ltrh\n')


# In[4]:


get_ipython().run_cell_magic('bash', '', 'cd /home/sam/data/Cvirginica\nls -lh\n')


# ### Concatenate files
# 
# Also renamed one file to maintain same naming structure as concatenated files.

# In[5]:


get_ipython().run_cell_magic('bash', '', 'cd /home/sam/data/Cvirginica\ncat \\\n2112_lane1_ACAGTG_L001_R1_001.fastq.gz \\\n2112_lane1_ACAGTG_L001_R1_002.fastq.gz \\\n> 2112_lane1_ACAGTG.fastq.gz\n\ncat \\\n2112_lane1_ATCACG_L001_R1_001.fastq.gz \\\n2112_lane1_ATCACG_L001_R1_002.fastq.gz \\\n2112_lane1_ATCACG_L001_R1_003.fastq.gz \\\n> 2112_lane1_ATCACG.fastq.gz\n\ncat \\\n2112_lane1_CAGATC_L001_R1_001.fastq.gz \\\n2112_lane1_CAGATC_L001_R1_002.fastq.gz \\\n2112_lane1_CAGATC_L001_R1_003.fastq.gz \\\n> 2112_lane1_CAGATC.fastq.gz\n\ncat \\\n2112_lane1_GCCAAT_L001_R1_001.fastq.gz \\\n2112_lane1_GCCAAT_L001_R1_002.fastq.gz \\\n> 2112_lane1_GCCAAT.fastq.gz\n\nmv \\\n2112_lane1_TGACCA_L001_R1_001.fastq.gz \\\n2112_lane1_TGACCA.fastq.gz\n\ncat \\\n2112_lane1_TTAGGC_L001_R1_001.fastq.gz \\\n2112_lane1_TTAGGC_L001_R1_002.fastq.gz \\\n> 2112_lane1_TTAGGC.fastq.gz\n\nsed \'/^Subject:/ s/ / concatenation JOB COMPLETE/\' ~/.default-subject.mail | msmtp "$EMAIL"\n')


# In[6]:


get_ipython().run_cell_magic('bash', '', 'cd /home/sam/data/Cvirginica\nls -lhtr\n')


# ### Move files around to improve organization

# In[7]:


get_ipython().run_cell_magic('bash', '', 'data=/home/sam/data/Cvirginica/\ndata_cat=/home/sam/data/Cvirginica/concatenated\nmkdir $data/concatenated\nmv $data/2112_lane1_TGACCA.fastq.gz $data_cat/\nmv $data/2112_lane1_ACAGTG.fastq.gz $data_cat/\nmv $data/2112_lane1_ATCACG.fastq.gz $data_cat/\nmv $data/2112_lane1_CAGATC.fastq.gz $data_cat/\nmv $data/2112_lane1_GCCAAT.fastq.gz $data_cat/\nmv $data/2112_lane1_TTAGGC.fastq.gz $data_cat/\n\nls -lh $data_cat\n')


# ### Run FastQC
# 
# The code belows creates a space-delimited list of the FastQ files (FASTQ_LIST).
# 
# This is then passed to FastQC.

# In[8]:


get_ipython().run_cell_magic('bash', '', 'data_cat=/home/sam/data/Cvirginica/concatenated\nmkdir $data_cat/20180910_Cvirginica_oil_fastqc\ncd $data_cat\n\nFASTQ_LIST="$(ls -1 *.gz| tr \'\\n\' \' \')"\ntime \\\n/home/shared/fastqc_v0.11.7/fastqc \\\n--extract \\\n--threads 16 \\\n--quiet \\\n--outdir $data_cat/20180910_Cvirginica_oil_fastqc \\\n$FASTQ_LIST\n\nsed \'/^Subject:/ s/ / fastqc JOB COMPLETE/\' ~/.default-subject.mail | msmtp "$EMAIL"\n')


# In[9]:


get_ipython().run_cell_magic('bash', '', 'cd /home/sam/data/Cvirginica/concatenated/20180910_Cvirginica_oil_fastqc/\nls\n')


# ### Run MultiQC.

# In[10]:


get_ipython().run_cell_magic('bash', '', 'cd /home/sam/data/Cvirginica/concatenated/20180910_Cvirginica_oil_fastqc/\ntime \\\nmultiqc .\nls\n')


# ### Files copied to Owl.
# 
# Performed outside of notebook, due to ```sudo``` requirement.

# In[11]:


get_ipython().run_cell_magic('bash', '', 'ls /mnt/owl/Athaliana/20180910_Cvirginica_oil_fastqc/\n')


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