comparison sirius_csifingerid.py @ 9:8dac4cef0a22 draft default tip

"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit c2fc3de462ef4bd1a225c41624b094c3b5874736"

8:7b9c17738db8

parser = argparse.ArgumentParser()
parser.add_argument('--input_pth')
parser.add_argument('--canopus_result_pth')
parser.add_argument('--annotations_result_pth')
parser.add_argument('--database')
parser.add_argument('--profile')
parser.add_argument('--candidates')
parser.add_argument('--ppm_max')
parser.add_argument('--polarity')

parser.add_argument('--out_dir')
parser.add_argument('--tool_directory')
parser.add_argument('--temp_dir')
parser.add_argument('--meta_select_col', default='all')
parser.add_argument('--cores_top_level', default=1)
parser.add_argument('--chunks', default=1)
parser.add_argument('--min_MSMS_peaks', default=1)
parser.add_argument('--rank_filter', default=0)
parser.add_argument('--confidence_filter', default=0)
parser.add_argument('--schema', default='msp')
parser.add_argument('-a', '--adducts', action='append', nargs=1,
                    required=False, default=[], help='Adducts used')

args = parser.parse_args()

# Setup parameter dictionary
######################################################################
def init_paramd(args):
    paramd = defaultdict()
    paramd["cli"] = {}
    paramd["cli"]["--database"] = args.database
    paramd["cli"]["--profile"] = args.profile
    paramd["cli"]["--candidates"] = args.candidates
    paramd["cli"]["--ppm-max"] = args.ppm_max
    if args.polarity == 'positive':

            in paramd['additional_details']):
        # If possible always good to have the adduct in output as a column
        paramd['additional_details']['adduct'] = adduct

    # ============== Create CLI cmd for metfrag ===============================
    cmd = "sirius --no-citations --ms2 {} --adduct {} --precursor {} -o {} " \
          "formula -c {} --ppm-max {} --profile {} " \
          "structure --database {} canopus".format(
                       paramd["cli"]["--ms2"],
                       adduct,
                       paramd["cli"]["--precursor"],
                       paramd["cli"]["--output"],
                       paramd["cli"]["--candidates"],

# Concatenate and filter the output
######################################################################
# outputs might have different headers. Need to get a list of all the headers
# before we start merging the files outfiles = [os.path.join(wd, f) for f in
# glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
def concat_output(filename, result_pth,
                  rank_filter, confidence_filter):
    outfiles = glob.glob(os.path.join(wd, '*', '*{}'.format(filename)))

    # sort files nicely
    outfiles.sort(key=lambda s: int(re.match(r'^.*/('
                                             r'\d+).*{}'.format(filename),
                                             s).group(1)))
    print(outfiles)

    if len(outfiles) == 0:
        print('No results')
        sys.exit()

    headers = []

            print(fn)

            with open(fn) as infile:
                reader = csv.DictReader(infile, delimiter='\t')

                ad = paramds[fn.split(os.sep)[-2]]['additional_details']

                for line in reader:
                    if 'rank' in line \
                            and 0 < int(rank_filter) < int(line['rank']):
                        # filter out those annotations greater than rank filter
                        # If rank_filter is zero then skip
                        continue

                    if 'ConfidenceScore' in line:
                        if isinstance(line['ConfidenceScore'], str):
                            # Value is NA or N/A
                            continue

                        if (0 < float(confidence_filter)
                            and float(line['ConfidenceScore'])
                                < float(confidence_filter)):
                            # filter out those annotations that are less than
                            # the confidence filter value
                            continue
                    line.update(ad)

                    dwriter.writerow(line)


concat_output('compound_identifications.tsv',
              args.annotations_result_pth,
              args.rank_filter,
              args.confidence_filter)
concat_output('canopus_summary.tsv',
              args.canopus_result_pth,
              0,
              0)

9:8dac4cef0a22

parser = argparse.ArgumentParser()
parser.add_argument('--input_pth')
parser.add_argument('--canopus_result_pth')
parser.add_argument('--annotations_result_pth')
parser.add_argument('--all_structures_result_pth')
parser.add_argument('--database')
parser.add_argument('--profile')
parser.add_argument('--candidates')
parser.add_argument('--ppm_max')
parser.add_argument('--polarity')

parser.add_argument('--out_dir')
parser.add_argument('--tool_directory')
parser.add_argument('--temp_dir')
parser.add_argument('--meta_select_col', default='all')
parser.add_argument('--cores_top_level', default=1)
parser.add_argument('--cores_sirius', default=4)
parser.add_argument('--chunks', default=1)
parser.add_argument('--min_MSMS_peaks', default=1)
parser.add_argument('--schema', default='msp')
parser.add_argument('-a', '--adducts', action='append', nargs=1,
                    required=False, default=[], help='Adducts used')

args = parser.parse_args()

# Setup parameter dictionary
######################################################################
def init_paramd(args):
    paramd = defaultdict()
    paramd["cli"] = {}
    paramd["cli"]["--cores"] = args.cores_sirius
    paramd["cli"]["--database"] = args.database
    paramd["cli"]["--profile"] = args.profile
    paramd["cli"]["--candidates"] = args.candidates
    paramd["cli"]["--ppm-max"] = args.ppm_max
    if args.polarity == 'positive':

            in paramd['additional_details']):
        # If possible always good to have the adduct in output as a column
        paramd['additional_details']['adduct'] = adduct

    # ============== Create CLI cmd for metfrag ===============================
    cmd = "sirius --cores {} --no-citations --ms2 {} --adduct {} " \
          "--precursor {} -o {} " \
          "formula -c {} --ppm-max {} --profile {} " \
          "structure --database {} canopus".format(
                       paramd["cli"]["--cores"],
                       paramd["cli"]["--ms2"],
                       adduct,
                       paramd["cli"]["--precursor"],
                       paramd["cli"]["--output"],
                       paramd["cli"]["--candidates"],

# Concatenate and filter the output
######################################################################
# outputs might have different headers. Need to get a list of all the headers
# before we start merging the files outfiles = [os.path.join(wd, f) for f in
# glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
def concat_output(wd, filename, result_pth, level=2):

    if level == 2:
        outfiles = glob.glob(os.path.join(wd, '*', filename))
    else:
        outfiles = glob.glob(os.path.join(wd, '*', '*', filename))

    outfiles.sort(
        key=lambda s: int(
            re.match(r'.*/([0-9]+).*/{}$'.format(filename),
                     s).group(1)))
    print(outfiles)
    if len(outfiles) == 0:
        print('No results')
        sys.exit()

    headers = []

            print(fn)

            with open(fn) as infile:
                reader = csv.DictReader(infile, delimiter='\t')

                ad = paramds[fn.split(os.sep)[-level]]['additional_details']

                for line in reader:

                    line.update(ad)

                    dwriter.writerow(line)


concat_output(wd,
              'compound_identifications.tsv',
              args.annotations_result_pth)

concat_output(wd,
              'canopus_summary.tsv',
              args.canopus_result_pth)

concat_output(wd,
              'structure_candidates.tsv',
              args.all_structures_result_pth,
              level=3)