comparison assembly_stats_txt.py @ 1:7556309ffbaf draft default tip

"planemo upload for repository https://github.com/phac-nml/galaxy_tools commit fb4c29f720748f46ff501140f2cd306bab6614f9"

0:ad2b274663f8

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

# Version 1.01 - bugs kindly corrected by Jan van Haarst
# Modified by Matthew Gopez October 13th, 2017

import logging
import os
import subprocess
import sys


log = logging.getLogger(__name__)

assert sys.version_info[:2] >= (2, 4)


def stop_err(msg):
    sys.stderr.write('%s\n' % msg)
    sys.exit()


def __main__():

    # Parse Command Line

    working_dir = sys.argv[2]
    type = sys.argv[3]
    bucket = sys.argv[4]
    input = sys.argv[5]
    stats = sys.argv[6]
    sortedcontigs = sys.argv[7]
    histogrampng = sys.argv[8]
    summedcontigspng = sys.argv[9]
    histogramdata = sys.argv[10]
    summedcontigdata = sys.argv[11]
    try:  # for test - needs this done
        os.makedirs(working_dir)
    except Exception, e:
        stop_err('Error running assembly_stats_txt.py ' + str(e))

    cmdline = '%s/fasta_summary.pl -i %s -t %s %s -o %s > /dev/null' \
        % (os.path.dirname(sys.argv[0]), input, type, bucket,
           working_dir)
    try:
        proc = subprocess.Popen(args=cmdline, shell=True,
                                stderr=subprocess.PIPE)
        returncode = proc.wait()

        # get stderr, allowing for case where it's very large

        stderr = ''
        buffsize = 1048576
        try:
            while True:
                stderr += proc.stderr.read(buffsize)
                if not stderr or len(stderr) % buffsize != 0:
                    break
        except OverflowError:
            pass
        if returncode != 0:
            raise Exception
    except Exception, e:
        stop_err('Error running assembly_stats.py ' + str(e))

    stats_path = os.path.join(working_dir, 'stats.txt')
    sorted_contigs_path = os.path.join(working_dir, 'sorted_contigs.fa')
    histogram_png_path = os.path.join(working_dir,
                                      'histogram_bins.dat.png')
    summed_contigs_path = os.path.join(working_dir,
                                       'summed_contig_lengths.dat.png')
    histogram_data_path = os.path.join(working_dir, 'histogram_bins.dat')
    summed_contigs_data_path = os.path.join(working_dir,
                                            'summed_contig_lengths.dat')

    out = open(stats, 'w')
    for line in open(stats_path):
        out.write('%s' % line)
    out.close()

    out = open(sortedcontigs, 'w')
    for line in open(sorted_contigs_path):
        out.write('%s' % line)
    out.close()

    out = open(histogrampng, 'w')
    for line in open(histogram_png_path):
        out.write('%s' % line)
    out.close()

    out = open(summedcontigspng, 'w')
    for line in open(summed_contigs_path):
        out.write('%s' % line)
    out.close()

    out = open(histogramdata, 'w')
    for line in open(histogram_data_path):
        out.write('%s' % line)
    out.close()

    out = open(summedcontigdata, 'w')
    for line in open(summed_contigs_data_path):
        out.write('%s' % line)
    out.close()


if __name__ == '__main__':
    __main__()

1:7556309ffbaf

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

# Version 1.01 - bugs kindly corrected by Jan van Haarst
# Modified by Matthew Gopez October 13th, 2017
# Rewritten by Matthew Gopez May 25th, 2020

import argparse
import os
import shutil
import subprocess
from pathlib import Path


PERL_OUT_FILES = ['stats.txt', 'sorted_contigs.fa', 'histogram_bins.dat.png',
                  'summed_contig_lengths.dat.png', 'histogram_bins.dat',
                  'summed_contig_lengths.dat']


def init_parser():
    """Create argument parser and return parser obj."""
    parser = argparse.ArgumentParser(description="usage: %prog [options]")

    parser.add_argument(
        "-d",
        "--working-dir",
        dest="working_dir",
        required=True)

    parser.add_argument(
        "-t",
        "--type",
        dest="file_type",
        required=True)

    parser.add_argument(
        "-b",
        "--bucket",
        dest="bucket",
        action='store_true')

    parser.add_argument(
        "-i",
        "--input",
        dest="input",
        required=True)

    parser.add_argument(
        "-s",
        "--stats",
        dest="stats",
        required=True)

    parser.add_argument(
        "-sc",
        "--sorted-contigs",
        dest="sorted_contigs",
        required=True)

    parser.add_argument(
        "-hpng",
        "--histogram-png",
        dest="histogram_png",
        required=True)

    parser.add_argument(
        "-spng",
        "--summed-contigs-png",
        dest="summed_contigs_png",
        required=True)

    parser.add_argument(
        "-hd",
        "--histogram-data",
        dest="histogram_data",
        required=True)

    parser.add_argument(
        "-scd",
        "--summed-config-data",
        dest="summed_contig_data",
        required=True)

    return parser


def exec_fasta_summary(input_data, file_type, bucket, working_dir):
    """Execute fasta_summary.pl script with user arguments."""
    script_dir = Path(__file__).parent.absolute()

    if bucket:
        bucket_arg = '-b'
    else:
        bucket_arg = ''

    cli_command = \
        '{}/fasta_summary.pl -i {} -t {} {} -o {} > /dev/null'.format(
            script_dir, input_data, file_type, bucket_arg, working_dir)

    try:
        subprocess.check_output(
            cli_command,
            stderr=subprocess.STDOUT,
            shell=True,
            universal_newlines=True)
    except subprocess.CalledProcessError as exc:
        raise RuntimeError('Error running assembly_stats.py!\n'
                           'Return Code: {}\nOutput: {}'.format(
                            exc.returncode, exc.output))


def main():
    """This is where the magic happens. (not really)

    1. Gets command line arguments.
    2. Grabs the user's desired parameters for running the perl script.
    3. Ensures the directories are in place.
    4. Executes fasta_summary.pl
    5. Move the out files from the perl script to the desired
    location the user specified.

    """
    parser = init_parser()
    args = parser.parse_args()

    working_dir = args.working_dir

    out_file_names = [args.stats, args.sorted_contigs, args.histogram_png,
                      args.summed_contigs_png, args.histogram_data,
                      args.summed_contig_data]

    # Ensure working directory is created.
    Path(working_dir).mkdir(parents=True, exist_ok=True)

    # Execute Perl Script
    exec_fasta_summary(args.input, args.file_type, args.bucket, working_dir)

    # Rename out files to desired file names
    for perl_out_file, dest_file in zip(PERL_OUT_FILES, out_file_names):
        shutil.move(os.path.join(working_dir, perl_out_file),
                    dest_file)


if __name__ == "__main__":
    main()