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

# ## Convert _P.generosa_ GFF to GTF
# 
# ### Notebook relies on:
# 
# - [GffRead](https://github.com/gpertea/gffread)
# 
# ### Addresses [this GitHub Issue](https://github.com/RobertsLab/resources/issues/1411)

# ### 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[1]:


# Set directories, input/output files
get_ipython().run_line_magic('env', 'data_dir=/home/sam/data/P_generosa/genomes')
get_ipython().run_line_magic('env', 'analysis_dir=/home/sam/analyses/20220301-pgen-gff_to_gtf')
analysis_dir="20220301-pgen-gff_to_gtf"

# Input files (from NCBI)
get_ipython().run_line_magic('env', 'gff=Panopea-generosa-v1.0.a4.gff3')

# URL to download files from NCBI
get_ipython().run_line_magic('env', 'url=https://gannet.fish.washington.edu/Atumefaciens/20191105_swoose_pgen_v074_renaming')

# Output file(s)
get_ipython().run_line_magic('env', 'gtf=Panopea-generosa-v1.0.a4.gtf')


# Set program locations
get_ipython().run_line_magic('env', 'gffread=/home/sam/programs/gffread-0.12.7.Linux_x86_64/gffread')


# ### Create analysis directory

# In[2]:


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')


# ### Download GFF

# In[3]:


get_ipython().run_cell_magic('bash', '', 'cd "${data_dir}"\n\n# Download with wget.\n# Use --quiet option to prevent wget output from printing too many lines to notebook\n# Use --continue to prevent re-downloading fie if it\'s already been downloaded.\n# Use --no-check-certificate to avoid download error from gannet\nwget --quiet \\\n--continue \\\n--no-check-certificate \\\n${url}/${gff}\n\nls -ltrh "${gff}"\n')


# ### Examine GFF

# In[4]:


get_ipython().run_cell_magic('bash', '', 'head -n 20 "${data_dir}"/"${gff}"\n')


# ### Convert GFF to GTF

# In[5]:


get_ipython().run_cell_magic('bash', '', 'cd "${data_dir}"\n\n${gffread} -E \\\n${data_dir}/"${gff}" -T \\\n1> ${analysis_dir}/"${gtf}" \\\n2> ${analysis_dir}/gffread-gff_to_gtf.stderr\n')


# ### Inspect GTF

# In[6]:


get_ipython().run_cell_magic('bash', '', 'head ${analysis_dir}/"${gtf}"\n')


# ### Generate checksum(s)

# In[7]:


get_ipython().run_cell_magic('bash', '', 'cd "${analysis_dir}"\n\nfor file in *\ndo\n  md5sum "${file}" | tee --append checksums.md5\ndone\n')


# ### Document GffRead program options

# In[8]:


get_ipython().run_cell_magic('bash', '', '${gffread} -h\n')


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