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

# ## Create _P.generosa_ tissue-specific lncRNA Expression Matrices
# 
# Use lncRNA GTF to ([from 20230502](https://robertslab.github.io/sams-notebook/2023/05/02/lncRNA-Identification-P.generosa-lncRNAs-using-CPC2-and-bedtools.html)) to determine lncRNA expression.
# 
# #### Notebook relies on:
# 
# - [`stringtie`](https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual)
# 
# 

# ### 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[3]:


# Set directories
get_ipython().run_line_magic('env', 'transcriptomes_dir=/home/shared/8TB_HDD_01/sam/data/P_generosa/transcriptomes')
get_ipython().run_line_magic('env', 'genomes_dir=/home/shared/8TB_HDD_01/sam/data/P_generosa/genomes')
get_ipython().run_line_magic('env', 'analysis_dir=/home/shared/8TB_HDD_01/sam/analyses/20230504-pgen-lncRNA-expression')
analysis_dir="20230504-pgen-lncRNA-expression"

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

# Average read length
get_ipython().run_line_magic('env', 'read_length=130')

# Input files
get_ipython().run_line_magic('env', 'lncRNA_gtf=20230502-pgen-lncRNA-IDs.gtf')
## lncRNA directory URL
## https://gannet.fish.washington.edu/Atumefaciens/20230502-pgen-lncRNA-identification/
get_ipython().run_line_magic('env', 'lncRNA_url=gannet:/volume2/web/Atumefaciens/20230502-pgen-lncRNA-identification')

## Tissue-specific sorted BAM files directory URL
## https://gannet.fish.washington.edu/Atumefaciens/20230426-pgen-HISAT2-stringtie-gffcompare-RNAseq/
get_ipython().run_line_magic('env', 'sorted_bams_url=gannet:/volume2/web/Atumefaciens/20230426-pgen-HISAT2-stringtie-gffcompare-RNAseq')


# Output file(s)
get_ipython().run_line_magic('env', 'lncRNA_stringtie_gtf=pgen-lncRNA-stringtie.gtf')

# Set program locations
get_ipython().run_line_magic('env', 'stringtie=/home/shared/stringtie-2.2.1.Linux_x86_64/stringtie')
get_ipython().run_line_magic('env', 'prepDE=/home/shared/stringtie-2.2.1.Linux_x86_64/prepDE.py3')

# Line for formatting
get_ipython().run_line_magic('env', 'line=-------------------------------------------------------------------------------------')


# ## Create analysis directories

# In[4]:


get_ipython().run_cell_magic('bash', '', '\ndeclare -a sample_names_array=(ctenidia gonad heart juvenile larvae)\n\nfor sample in "${sample_names_array[@]}"\ndo\n  # Make analysis and data directory, if doesn\'t exist\n  mkdir --parents "${analysis_dir}/${sample}"\ndone\n\nls -l "${analysis_dir}"\n')


# ## Download lncRNA GTF

# In[5]:


get_ipython().run_cell_magic('bash', '', 'cd "${transcriptomes_dir}"\n\nrsync "${lncRNA_url}/${lncRNA_gtf}" .\n\n\nls -ltrh "${lncRNA_gtf}"\n')


# ### Inspect GTF

# In[6]:


get_ipython().run_cell_magic('bash', '', 'head "${transcriptomes_dir}/${lncRNA_gtf}"\n\necho ""\necho "${line}"\necho ""\n\necho "Number of lines:"\nwc -l "${transcriptomes_dir}/"*.gtf\n')


# ## Download tissue-specific BAM files

# In[7]:


get_ipython().run_cell_magic('bash', '', 'declare -a sample_names_array=(ctenidia gonad heart juvenile larvae)\ncd "${transcriptomes_dir}"\n\nfor sample in "${sample_names_array[@]}"\ndo\n  rsync -avP "${sorted_bams_url}/${sample}/*.bam" ./"${sample}"/\ndone\n\n\ntree -h\n')


# ## Run StingTie to calculate expression values

# In[8]:


get_ipython().run_cell_magic('bash', '', 'declare -a sample_names_array=(ctenidia gonad heart juvenile larvae)\ncd "${transcriptomes_dir}"\n\ntime \\\nfor sample in "${sample_names_array[@]}"\ndo\n  "${stringtie}" \\\n    -G "${lncRNA_gtf}" \\\n    -e "${sample}/${sample}.sorted.bam" \\\n    -B \\\n    -o "${analysis_dir}/${sample}/${sample}-${lncRNA_stringtie_gtf}" \\\n    -p "${threads}"\ndone\n')


# ### Inspect Ballgown `t_data.ctab` files

# In[9]:


get_ipython().run_cell_magic('bash', '', 'declare -a sample_names_array=(ctenidia gonad heart juvenile larvae)\ncd "${analysis_dir}"\n\nfor sample in "${sample_names_array[@]}"\ndo\n  head --verbose "${sample}/t_data.ctab" | column -t\ndone\n')


# ## Create count matrix

# In[10]:


get_ipython().run_cell_magic('bash', '', 'cd "${analysis_dir}"\n\n"${prepDE}" \\\n-l "${read_length}"\n\nls -ltrh\n')


# ### Inspect transcript counts

# In[11]:


get_ipython().run_cell_magic('bash', '', 'cd "${analysis_dir}"\n\nhead transcript_count_matrix.csv | column -t -s ","\n\necho ""\necho "${line}"\necho ""\n\nwc -l transcript_count_matrix.csv\n')