comparison msconvert_wrapper.py @ 6:6b6bba73eadb draft

planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848

5:637e309295cf

import tempfile
import shutil
import subprocess
import re
import logging

assert sys.version_info[:2] >= (2, 6)

log = logging.getLogger(__name__)
working_directory = os.getcwd()

def execute(command, stdin=None):
    try:
        with open(tmp_stderr_name, 'wb') as tmp_stderr:
            with open(tmp_stdout_name, 'wb') as tmp_stdout:
                proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
                returncode = proc.wait()
                if returncode != 0:
                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
    finally:
        print(( open(tmp_stderr_name, "r").read() ))

def __main__():
    run_script()

#ENDTEMPLATE

to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2']


def str_to_bool(v):
    """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
    return v.lower() in ["yes", "true", "t", "1"]

    if debug:
        print(( open(filters_file_path, "r").read() ))
    return filters_file_path


def _build_base_cmd(options):
    to_extension = options.toextension
    if to_extension.startswith("unindexed_"):
        to_extension = to_extension[len("unindexed_"):]
        to_params = "--noindex"
    else:
        to_params = ""
    cmd = "msconvert --%s %s" % (to_extension, to_params)
    if str_to_bool(options.zlib):
        cmd = "%s %s" % (cmd, "--zlib")
    if options.binaryencoding:
        cmd = "%s --%s" % (cmd, options.binaryencoding)
    if options.mzencoding:

def run_script():
    parser = optparse.OptionParser()
    parser.add_option('--input', dest='inputs', action='append', default=[])
    parser.add_option('--input_name', dest='input_names', action='append', default=[])
    parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the msconvert command line.')
    parser.add_option('--output', dest='output')
    parser.add_option('--fromextension', dest='fromextension')
    parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
    parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
    parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])

        input_file = input_file
        copy_to_working_directory(input, input_file)
        if input in options.implicits:
            continue
        input_files.append(input_file)

    cmd = _build_base_cmd(options)
    file_column = options.filter_table_file_column
    if not file_column:
        # Apply same filters to all files, just create a unviersal filter files
        # and run msconvert once.
        filters_file_path = _create_filters_file(options, debug=options.debug)

        input_files = filtered_files
    if len(input_files) > 1:
        cmd = "%s --merge" % cmd
    output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug)
    shutil.copy(output_file, options.output)


if __name__ == '__main__':
    __main__()

6:6b6bba73eadb

import tempfile
import shutil
import subprocess
import re
import logging
import shlex

assert sys.version_info[:2] >= (2, 6)

log = logging.getLogger(__name__)
working_directory = os.getcwd()

def execute(command, stdin=None):
    try:
        with open(tmp_stderr_name, 'wb') as tmp_stderr:
            with open(tmp_stdout_name, 'wb') as tmp_stdout:
                args = shlex.split(command) # handle proper splitting of quoted args
                proc = subprocess.Popen(args=args, shell=False, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
                returncode = proc.wait()
                if returncode != 0:
                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
    finally:
        print(( open(tmp_stderr_name, "r").read() ))

def __main__():
    run_script()

#ENDTEMPLATE

to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'mz5', 'txt', 'ms2', 'cms2']


def str_to_bool(v):
    """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """
    return v.lower() in ["yes", "true", "t", "1"]

    if debug:
        print(( open(filters_file_path, "r").read() ))
    return filters_file_path


def _build_base_cmd(options,args=None):
    to_extension = options.toextension
    if to_extension.startswith("unindexed_"):
        to_extension = to_extension[len("unindexed_"):]
        to_params = "--noindex"
    else:
        to_params = ""
    cmd = "msconvert --%s %s" % (to_extension, to_params)
    if args:
        cmd = "%s %s" % (cmd, ' '.join(args))
    if str_to_bool(options.zlib):
        cmd = "%s %s" % (cmd, "--zlib")
    if options.binaryencoding:
        cmd = "%s --%s" % (cmd, options.binaryencoding)
    if options.mzencoding:

def run_script():
    parser = optparse.OptionParser()
    parser.add_option('--input', dest='inputs', action='append', default=[])
    parser.add_option('--input_name', dest='input_names', action='append', default=[])
    parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the msconvert command line.')
    parser.add_option('--ident', dest='idents', action='append', default=[])
    parser.add_option('--ident_name', dest='ident_names', action='append', default=[])
    parser.add_option('--output', dest='output')
    parser.add_option('--refinement', dest='refinement')
    parser.add_option('--fromextension', dest='fromextension')
    parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions)
    parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64'])
    parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64'])
    parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64'])

        input_file = input_file
        copy_to_working_directory(input, input_file)
        if input in options.implicits:
            continue
        input_files.append(input_file)
    for i, ident in enumerate(options.idents):
        ident_file = options.ident_names[i]
        copy_to_working_directory(ident, ident_file)

    cmd = _build_base_cmd(options,args=args)
    file_column = options.filter_table_file_column
    if not file_column:
        # Apply same filters to all files, just create a unviersal filter files
        # and run msconvert once.
        filters_file_path = _create_filters_file(options, debug=options.debug)

        input_files = filtered_files
    if len(input_files) > 1:
        cmd = "%s --merge" % cmd
    output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug)
    shutil.copy(output_file, options.output)
    if options.refinement:
        # .mzRefinement.tsv
        files = os.listdir(os.getcwd())
        for fname in files:
            if fname.endswith('.mzRefinement.tsv'):
                shutil.copy(fname, options.refinement)
                break

def __main__():
    run_script()

if __name__ == '__main__':
    __main__()