view peptide_pi_annotator.py @ 3:78afc81ab244 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit decb06dc90d7069d317968b979f649a04720b264

#!/usr/bin/env python

import re
import sys
import argparse


def main():
    if sys.argv[1:] == []:
        sys.argv.append('-h')
    args = parse_commandline()
    strips = {}
    if args.frac_col > 0:
        frac_col = args.frac_col - 1
    elif args.frac_col:
        frac_col = args.frac_col
    elif args.frac_colpattern:
        frac_col = get_col_by_pattern(args.peptable, args.frac_colpattern)
    else:
        raise RuntimeError('Must define fraction column')
    if args.stripcol > 0:
        stripcol = args.stripcol - 1
    elif args.stripcol:
        stripcol = args.stripcol
    elif args.stripcolpattern:
        stripcol = get_col_by_pattern(args.peptable, args.stripcolpattern)
    else:
        raise RuntimeError('Must define strip column')
    if args.pepcol:
        pepcol = args.pepcol - 1
    elif args.pepcolpattern:
        pepcol = get_col_by_pattern(args.peptable, args.pepcolpattern)
    else:
        raise RuntimeError('Must define peptide sequence column')
    for i, strip in enumerate(args.pipatterns):
        strips[strip] = {'intercept': args.intercepts[i],
                         'fr_width': args.fr_width[i]}
    with open(args.outpeptable, 'w') as fp:
        for outline in annotate_peptable(args.pipeps, args.peptable, pepcol,
                                         frac_col, stripcol, strips,
                                         args.ignoremods):
            fp.write('\t'.join([str(x) for x in outline]))
            fp.write('\n')


def get_strip(strips, string):
    for pattern in strips.keys():
        if re.search(pattern, string):
            return strips[pattern]
    return False


def get_col_by_pattern(peptable, colpattern):
    with open(peptable) as fp:
        header = next(fp).strip('\n').split('\t')
    for ix, field in enumerate(header):
        if colpattern in field:
            return ix


def annotate_peptable(predicted_peps_fn, peptable, seqcol, frac_col, stripcol,
                      strips, ignoremods):
    predicted_peps = {}
    with open(predicted_peps_fn) as fp:
        for line in fp:
            line = line.strip('\n').split('\t')
            predicted_peps[line[0]] = line[1]
    not_predicted_count, predicted_count = 0, 0
    with open(peptable) as fp:
        header = next(fp).strip('\n').split('\t')
        yield header + ['Experimental pI', 'Predicted pI', 'Delta pI']
        for line in fp:
            line = line.strip('\n').split('\t')
            sequence = line[seqcol]
            for weight in ignoremods:
                if weight == '*':
                    regex = '[+-]\d*\.\d*'
                else:
                    regex = '[+-]{}'.format(weight)
                sequence = re.sub(regex, '', sequence)
            try:
                pred_pi = float(predicted_peps[sequence])
            except KeyError:
                print('CANNOT PREDICT', sequence)
                not_predicted_count += 1
                pred_pi, delta_pi = 'NA', 'NA'
            else:
                predicted_count += 1
            strip = get_strip(strips, line[stripcol])
            if not strip:
                exp_pi, delta_pi = 'NA', 'NA'
            else:
                try:
                    exp_pi = (strip['fr_width'] * int(line[frac_col]) +
                              strip['intercept'])
                except ValueError:
                    print('Cannot detect fraction for PSM {}'.format(sequence))
                    exp_pi, delta_pi = 'NA', 'NA'
                else:
                    if pred_pi != 'NA':
                        delta_pi = exp_pi - pred_pi
                    else:
                        delta_pi = 'NA'
            yield line + [exp_pi, pred_pi, delta_pi]
    print('Number of peptides without pI prediction: {}\n'
          'Number of peptides predicted: {}\n'.format(not_predicted_count,
                                                      predicted_count))


def parse_commandline():
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument('--out', dest='outpeptable', help='Output peptide '
                        'table')
    parser.add_argument('-p', dest='peptable', help='Peptide/PSM table with '
                        'peptides, FDR, fraction numbers. Used to calculate'
                        'pI shift.')
    parser.add_argument('-i', dest='pipeps', help='A tab-separated txt file '
                        'with peptide seq, pI value')
    parser.add_argument('--pepcolpattern', dest='pepcolpattern',
                        help='Peptide sequence column pattern in peptide '
                        'table.', default=False, type=str)
    parser.add_argument('--pepcol', dest='pepcol', help='Peptide sequence '
                        'column number in peptide table. First column is 1.',
                        default=False, type=int)
    parser.add_argument('--fraccolpattern', dest='frac_colpattern',
                        help='Fraction number column pattern in peptide '
                        'table.', default=False, type=str)
    parser.add_argument('--fraccol', dest='frac_col', help='Fraction number '
                        'column number in peptide table. First column is 1.',
                        default=False, type=int)
    parser.add_argument('--ignoremods', dest='ignoremods', help='Regex to '
                        'identify modification weights to be ignored.',
                        default=[], nargs='+', type=str)
    parser.add_argument('--stripcolpattern', dest='stripcolpattern',
                        help='Strip name column pattern in peptide '
                        'table.', type=str, default=False)
    parser.add_argument('--stripcol', dest='stripcol', help='Strip name '
                        'column number in peptide table. Will be used to '
                        'detect strips if multiple are present using pattern '
                        'passed with --strippatterns. First column is nr. 1.',
                        default=False, type=int)
    parser.add_argument('--strippatterns', dest='pipatterns',
                        help='Patterns to detect different pI ranges from e.g.'
                        ' file name in peptide table', nargs='+')
    parser.add_argument('--intercepts', dest='intercepts',
                        help='pI Intercept of strips', nargs='+', type=float)
    parser.add_argument('--widths', dest='fr_width', nargs='+',
                        help='Strip fraction widths in pI', type=float)
    return parser.parse_args(sys.argv[1:])


if __name__ == '__main__':
    main()