annotate cuffmerge_wrapper.py @ 12:1707a530e598 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f

#!/usr/bin/env python

import optparse
import os
import shutil
import subprocess
import sys
import tempfile


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


def __main__():
    parser = optparse.OptionParser()
    parser.add_option('-g', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.')
    parser.add_option('-s', dest='use_seq_data', action="store_true", help='Causes cuffmerge to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.')
    parser.add_option('-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.')

    # Wrapper / Galaxy options.
    parser.add_option('', '--index', dest='index', help='The path of the reference genome')
    parser.add_option('', '--ref_file', dest='ref_file', help='The reference dataset from the history')

    # Outputs.
    parser.add_option('', '--merged-transcripts', dest='merged_transcripts')
    parser.add_option('--min-isoform-fraction', dest='min_isoform_fraction')

    (options, args) = parser.parse_args()

    # output version # of tool
    try:
        with tempfile.NamedTemporaryFile() as tmp_stdout:
            returncode = subprocess.call(args='cuffmerge -v 2>&1', stdout=tmp_stdout, shell=True)
            stdout = None
            with open(tmp_stdout.name) as tmp_stdout2:
                for line in tmp_stdout2:
                    if line.lower().find('merge_cuff_asms v') >= 0:
                        stdout = line.strip()
                        break
        if stdout:
            sys.stdout.write('%s\n' % stdout)
        else:
            raise Exception
    except:
        sys.stdout.write('Could not determine Cuffmerge version\n')

    # Set/link to sequence file.
    if options.use_seq_data:
        if options.ref_file:
            # Sequence data from history.
            # Create symbolic link to ref_file so that index will be created in working directory.
            seq_path = "ref.fa"
            os.symlink(options.ref_file, seq_path)
        else:
            if not os.path.exists(options.index):
                stop_err('Reference genome %s not present, request it by reporting this error.' % options.index)
            seq_path = options.index

    # Build command.

    # Base.
    cmd = "cuffmerge -o cm_output "

    # Add options.
    if options.num_threads:
        cmd += (" -p %i " % int(options.num_threads))
    if options.ref_annotation:
        cmd += " -g %s " % options.ref_annotation
    if options.use_seq_data:
        cmd += " -s %s " % seq_path
    if options.min_isoform_fraction:
        cmd += " --min-isoform-fraction %s " % (options.min_isoform_fraction)
    # Add input files to a file.
    with tempfile.NamedTemporaryFile(mode='w', dir=".", delete=False) as inputs_file:
        for arg in args:
            inputs_file.write(arg + "\n")
    cmd += inputs_file.name

    # Run command.
    try:
        with tempfile.NamedTemporaryFile(dir=".") as tmp_stderr:
            returncode = subprocess.call(args=cmd, stderr=tmp_stderr, shell=True)

            # Error checking.
            if returncode != 0:
                # Get stderr, allowing for case where it's very large.
                buffsize = 1048576
                stderr = ''
                with open(tmp_stderr.name, 'r') as tmp_stderr2:
                    try:
                        while True:
                            stderr += tmp_stderr2.read(buffsize)
                            if not stderr or len(stderr) % buffsize != 0:
                                break
                    except OverflowError:
                        pass
                raise Exception(stderr)

        if len(open("cm_output/merged.gtf", 'r').read().strip()) == 0:
            raise Exception('The output file is empty, there may be an error with your input file or settings.')

        # Copy outputs.
        shutil.move("cm_output/merged.gtf", options.merged_transcripts)
    except Exception as e:
        stop_err('Error running cuffmerge: %s' % e)


if __name__ == "__main__":
    __main__()