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

# 

# In[1]:


get_ipython().system('date')


# In[2]:


get_ipython().run_cell_magic('bash', '', 'system_profiler SPSoftwareDataType\n')


# In[128]:


cd /Volumes/nightingales/O_lurida/20160203_mbdseq/


# ### Concatenate entire set of FASTQ files for each individual

# ##### The commands below use a for loop to:
# 1. process each FASTQ corresponding to an individual (zr1394_n_*)
# 2. concatenate each file (cat \$file) to the designated output file (\${file/_s*_R1/})
# 
# The output file is named using bash parameter expansion. It takes the file name ($file) and replaces the designated matching text (_s*_R1) with whatever follows the last slash - in this case, it's replaced with an empty string (i.e. deleted).

# In[129]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_1_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[130]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_2_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[131]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_3_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[132]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_4_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[133]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_5_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[134]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_6_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[135]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_7_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[136]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_8_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[137]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_9_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[138]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_10_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[139]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_11_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[140]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_12_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[141]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_13_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[142]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_14_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[143]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_15_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[144]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_16_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[145]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_17_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[146]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_18_*; do\n  cat $file >> ${file/_s*_R1/}\ndone\n')


# In[147]:


get_ipython().run_cell_magic('bash', '', '\nls -lh zr1394_{1..18}.fastq.gz\n')


# ### Concatenate sets of s4, s5, & s6 of FASTQ files for each individual

# ##### The commands below use a for loop to:
# 1. process the s4, s5, & s6 FASTQ corresponding to an individual (zr1394_1_s{4..6}*)
# 2. concatenate each file (cat \$file) to the designated output file (\${file/_s*_R1/_s456})
# 
# The output file is named using bash parameter expansion. It takes the file name ($file) and replaces the designated matching text (_s*_R1) with whatever follows the last slash - in this case, it's replaced with "_s456".

# In[148]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_1_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[149]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_2_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[150]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_3_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[151]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_4_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[152]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_5_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[153]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_6_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[154]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_7_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[155]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_8_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[156]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_9_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[157]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_10_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[158]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_11_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[159]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_12_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[160]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_13_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[161]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_14_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[162]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_15_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[163]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_16_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[164]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_17_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[165]:


get_ipython().run_cell_magic('bash', '', '\nfor file in zr1394_18_s{4..6}*; do\n  cat $file >> ${file/_s*_R1/_s456}\ndone\n')


# In[166]:


ls -lh zr1394_*_s456.fastq.gz | sort