Objective

The final program that you will have to write is expected to do the following things:

• Load a gtf file (e.g. this one)
• Compute the size of introns.
• Draw the distribution of intron size.

Constrains

• If needed/possible, use regular expression (e.g. to extract transcript name).
• Use an argument parser so that one can call it from command line.
• The color of the diagram should be proposed as an argument to the parser.

Note about regular expressions

In the regular expression below ([^"]+) the parentheses are used to capture a motif (here, a succession of characters that are different from ‘"’. The found motif can be recovered using the group() method.

import re
a_string = 'cds_id "cds1"; transcript_id "tx1"; gene_id "g1";'
hit = re.search('transcript_id "([^"]+)"', a_string)
if hit:
  print(hit.group(1))

## tx1

Note about argument parser

The argument parser can be used

# Declare an argument parser
import argparse 
DESCRIPTION = "The program description."
parser = argparse.ArgumentParser(add_help=True, description=DESCRIPTION)
parser.add_argument('-i', '--inputfile',
                            help="The input file.",
                            default=None,
                            type=argparse.FileType('r'),
                            required=True)
parser.add_argument('-o', '--outputfile',
                            help="The outputfile.",
                            default=None,
                            type=argparse.FileType('r'),
                            required=True)
parser.add_argument('-c', '--color',
                            help="The color of the diagram.",
                            default="magenta",
                            type=str,
                            required=False)
args = parser.parse_args()
args = dict(args.__dict__)