make_deliverable.py

#!/usr/bin/python

import os
import sys
import argparse
import textwrap
import subprocess


# TODO: Moved out of its initial folder, so some stuf (e.g. paths) may not work

__version__ = '1.0'


def eval_projects(projects):
    try:
        # Get the part of the project name that should be common
        proj = ['_'.join(p.split('_')[2:6]) for p in projects]

        # Count how many times the 1st element occurs.
        # If equal to the list length, then all elements
        # are the same (as should)
        return proj.count(proj[0]) == len(proj)
    except IndexError:
        print("Error! Make sure the project name(s) you gave are valid.")
        exit(1)

def make_deliverable(args):
    target_dir = 'deliverables'
    if os.path.exists(target_dir):
        os.chdir(target_dir)
    else:
        print("'{0}' directory does not exist. Exiting...".format(target_dir))
        exit(1)

    if not eval_projects(args.project):
        print("Error! Make sure the projects are \
                part of a bigger biological project.")
        print("Use --help for more information.")
        exit(1)

    if args.output is None:
        args.output = '_'.join(args.project[0].split('_')[2:7])

    # Create the deliverable directory for the project, and move to it
    try:
        os.mkdir(args.output)
    except OSError as e:
        print(e)
        exit(1)
    finally:
        os.chdir(args.output)

    print(os.getcwd())

    # Create 'fastq_files' directory if fastq argument was set
    if args.fastq:
        args.fastq = 'fastq_files'
        os.mkdir(args.fastq)

    # Get a dictionary of listed (sample) directories in each project
    #sample_dirs = {}
    projects_dir = '../../projects/'

    cmd = 'rsync -r --progress {0} {1}'

    for project in args.project:
        # Form the dir to get the data from
        source_dir = os.path.join(projects_dir, project + '/', 'counts/')
        # print(source_dir)

        p = subprocess.Popen(cmd.format(source_dir + '*', '.'),
                            shell=True).wait()

        # Copy the fastq files if the fastq argument was set
        if args.fastq:
            source_dir = os.path.join(projects_dir, project + '/', 'fastqs/')

            p = subprocess.Popen(cmd.format(source_dir + '*', args.fastq),
                                shell=True).wait()

def main():
    # Move the working directory to the local root folder
    # NOTE: Use when you call this script by running a link (softlink).
    # os.chdir(os.path.dirname(sys.path[0]))

    # Create a text wrapper for the help output text
    w = textwrap.TextWrapper(width=90,
                             break_long_words=False,
                             replace_whitespace=False)

    help_descr = "This script is used to create deliverables for the given projects"

    # Initialize a parser
    parser = argparse.ArgumentParser(
                 description=help_descr,
                 formatter_class=argparse.RawDescriptionHelpFormatter)

    # -- Add the appropriate arguments -- #
    parser.add_argument(
            '-v', '--version',
            action='version',
            version='%(prog)s {0}'.format(__version__))

    parser.add_argument(
            '-f', '--fastq', action='store_const', const=True,
            help='If set, it will also include the fastqs in the deliverable.')

    parser.add_argument(
            '-p', '--project', nargs='*', required=True,
            help='Names of the projects you want to include in the deliverable.\
            You can give multiple projects by simply separete them with space.\
            Note that the projects should be part of a bigger biological project.\
            In other words, this part of the name: 10X_YY_NNN_## should be common.')

    parser.add_argument(
            '-o', '--output',
            help='(Optional) The name of the deliverable to be created.')

    # Parse the given arguments
    args = parser.parse_args()

    # Call the function make_deliverable() to create the desired output
    make_deliverable(args)


if __name__ == '__main__':
    main()