comparison cufflinks_wrapper.py @ 11:e04dbae2abe0 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

10:83bec71c5c9f

import shutil
import subprocess
import sys
import tempfile

from galaxy.datatypes.util.gff_util import gff_attributes_to_str, parse_gff_attributes


def stop_err(msg):
    sys.exit("%s\n" % msg)

    # Global model (for trackster).
    parser.add_option('', '--global_model', dest='global_model_file', help='Global model used for computing on local data')

    (options, args) = parser.parse_args()

    # output version # of tool
    try:
        with tempfile.NamedTemporaryFile() as tmp_stdout:
            returncode = subprocess.call(args='cufflinks --no-update-check 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('cufflinks v') >= 0:
                        stdout = line.strip()
                        break
        if stdout:
            sys.stdout.write('%s\n' % stdout)
        else:
            raise Exception
    except:
        sys.stdout.write('Could not determine Cufflinks version\n')

    # If doing bias correction, set/link to sequence file.
    if options.do_bias_correction:
        if options.ref_file:
            # Sequence data from history.

11:e04dbae2abe0

import shutil
import subprocess
import sys
import tempfile


def parse_gff_attributes( attr_str ):
    """
    Parses a GFF/GTF attribute string and returns a dictionary of name-value
    pairs. The general format for a GFF3 attributes string is

        name1=value1;name2=value2

    The general format for a GTF attribute string is

        name1 "value1" ; name2 "value2"

    The general format for a GFF attribute string is a single string that
    denotes the interval's group; in this case, method returns a dictionary
    with a single key-value pair, and key name is 'group'
    """
    attributes_list = attr_str.split(";")
    attributes = {}
    for name_value_pair in attributes_list:
        # Try splitting by '=' (GFF3) first because spaces are allowed in GFF3
        # attribute; next, try double quotes for GTF.
        pair = name_value_pair.strip().split("=")
        if len( pair ) == 1:
            pair = name_value_pair.strip().split("\"")
        if len( pair ) == 1:
            # Could not split for some reason -- raise exception?
            continue
        if pair == '':
            continue
        name = pair[0].strip()
        if name == '':
            continue
        # Need to strip double quote from values
        value = pair[1].strip(" \"")
        attributes[ name ] = value

    if len( attributes ) == 0:
        # Could not split attributes string, so entire string must be
        # 'group' attribute. This is the case for strictly GFF files.
        attributes['group'] = attr_str
    return attributes


def gff_attributes_to_str( attrs, gff_format ):
    """
    Convert GFF attributes to string. Supported formats are GFF3, GTF.
    """
    if gff_format == 'GTF':
        format_string = '%s "%s"'
        # Convert group (GFF) and ID, parent (GFF3) attributes to transcript_id, gene_id
        id_attr = None
        if 'group' in attrs:
            id_attr = 'group'
        elif 'ID' in attrs:
            id_attr = 'ID'
        elif 'Parent' in attrs:
            id_attr = 'Parent'
        if id_attr:
            attrs['transcript_id'] = attrs['gene_id'] = attrs[id_attr]
    elif gff_format == 'GFF3':
        format_string = '%s=%s'
    attrs_strs = []
    for name, value in attrs.items():
        attrs_strs.append( format_string % ( name, value ) )
    return " ; ".join( attrs_strs )


def stop_err(msg):
    sys.exit("%s\n" % msg)

    # Global model (for trackster).
    parser.add_option('', '--global_model', dest='global_model_file', help='Global model used for computing on local data')

    (options, args) = parser.parse_args()

    # If doing bias correction, set/link to sequence file.
    if options.do_bias_correction:
        if options.ref_file:
            # Sequence data from history.