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

# # Compare E5 coral sRNA-seq trimming options
# 
# Simple adapter trimming vs. adapter trimming and trimming to expect sRNA lengths.
# 

# ### List computer specs

# 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')


# ### Set variables
# - `%env` indicates a bash variable
# 
# - without `%env` is Python variable

# In[2]:


# Set directories, input/output files
get_ipython().run_line_magic('env', 'data_dir=/home/shared/8TB_HDD_01/sam/data/A_pulchra/sRNAseq')
get_ipython().run_line_magic('env', 'analysis_dir=/home/shared/8TB_HDD_01/sam/analyses/20230524-E5-coral-sRNAseq_trimmings_comparisons')
analysis_dir="/home/shared/8TB_HDD_01/sam/20230524-E5-coral-sRNAseq_trimmings_comparisons"

get_ipython().run_line_magic('env', 'R1_fastq=/home/shared/8TB_HDD_01/sam/data/A_pulchra/sRNAseq/sRNA-ACR-140-S1-TP2_R1_001.fastq.gz')
get_ipython().run_line_magic('env', 'R2_fastq=/home/shared/8TB_HDD_01/sam/data/A_pulchra/sRNAseq/sRNA-ACR-140-S1-TP2_R2_001.fastq.gz')

# Set CPU threads
get_ipython().run_line_magic('env', 'threads=40')

# Max read length
get_ipython().run_line_magic('env', 'max_read_length=50')

# Set program locations
get_ipython().run_line_magic('env', 'fastqc=/home/shared/FastQC/fastqc')
get_ipython().run_line_magic('env', 'flexbar=/home/shared/flexbar-3.5.0-linux/flexbar')

# Set some formatting stuff
get_ipython().run_line_magic('env', 'break_line=--------------------------------------------------------------------------')


# ### Create analysis directory

# In[3]:


get_ipython().run_cell_magic('bash', '', '# Make analysis and data directory, if doesn\'t exist\nmkdir --parents "${analysis_dir}"\n\nmkdir --parents "${data_dir}"\n')


# # Adapter only trimming

# ### Inspect NEB Adapter FastA
# 
# Adapter sequences are in the NEB sRNA kit protocol used by Azenta for library construction.

# In[4]:


get_ipython().run_cell_magic('bash', '', 'cat "${data_dir}/NEB-adapters.fasta"\n')


# ### Trim adapters
# 
# Options:
# 
# - `-ap`: For paired-end analysis; recommended by NEB
# 
# - `-qf il.8`: Sets quality type as Illumina v1.8
# 
# - `qt`: Mean quality score of 25
# 
# - `--target`: Sets output filename
# 
# - `--zip-output GZ`: Sets gzip compression for trimmed files

# In[5]:


get_ipython().run_cell_magic('bash', '', 'cd ${analysis_dir}\n\n${flexbar} \\\n-r ${R1_fastq} \\\n-p ${R2_fastq}  \\\n-a ${data_dir}/NEB-adapters.fasta \\\n-ap ON \\\n-qf i1.8 \\\n-qt 25 \\\n--threads ${threads} \\\n--target sRNA-ACR-140-S1-TP2_R1_001-adapter_trim_only \\\n--zip-output GZ\n\nls -lh\n')


# ### Check log file

# In[6]:


get_ipython().run_cell_magic('bash', '', 'cd ${analysis_dir}\n\ncat sRNA-ACR-140-S1-TP2_R1_001-adapter_trim_only.log\n')


# # Adapter and length trimming

# ### Trim adapters and set max length (trimmed from 3' end)

# Options:
# 
# - `-ap`: For paired-end analysis; recommended by NEB
# 
# - `-qf il.8`: Sets quality type as Illumina v1.8
# 
# - `qt`: Mean quality score of 25
# 
# - `--post-trim-length`: Trim reads from 3' end to length specified after adapter and quality trimming.
# 
# - `--target`: Sets output filename
# 
# - `--zip-output GZ`: Sets gzip compression for trimmed files

# In[7]:


get_ipython().run_cell_magic('bash', '', 'cd ${analysis_dir}\n\n${flexbar} \\\n-r ${R1_fastq} \\\n-p ${R2_fastq}  \\\n-a ${data_dir}/NEB-adapters.fasta \\\n-ap ON \\\n-qf i1.8 \\\n-qt 25 \\\n--post-trim-length ${max_read_length} \\\n--threads ${threads} \\\n--target sRNA-ACR-140-S1-TP2_R1_001-adapter-and-length-50 \\\n--zip-output GZ\n\nls -lh\n')


# ### Check log file

# In[8]:


get_ipython().run_cell_magic('bash', '', 'cd ${analysis_dir}\n\ncat sRNA-ACR-140-S1-TP2_R1_001-adapter-and-length-50.log\n')


# # FastQC

# In[9]:


get_ipython().run_cell_magic('bash', '', 'cd ${analysis_dir}\n\ntrimmed_fastq_array=(*.fastq.gz)\n\n# Pass array contents to new variable as space-delimited list\ntrimmed_fastqc_list=$(echo "${trimmed_fastq_array[*]}")\n\n${fastqc} \\\n${trimmed_fastqc_list} \\\n--threads ${threads} \\\n--outdir ./ \\\n--quiet\n')


# # MultiQC

# In[10]:


get_ipython().run_cell_magic('bash', '', 'cd ${analysis_dir}\n\nmultiqc .\n')


# ### Document program options

# In[11]:


get_ipython().run_cell_magic('bash', '', '${flexbar} -hh\n')