Mercurial > repos > galaxyp > hirieftools

annotate peptide_pi_annotator.py @ 0:34c5c95740a1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
author galaxyp
date Mon, 22 May 2017 05:08:23 -0400
parents
children 8a30d6e5b97d
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34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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1 #!/usr/bin/env python
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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2
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3 import re
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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4 import sys
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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5 import argparse
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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6
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7
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8 def main():
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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9 if sys.argv[1:] == []:
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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10 sys.argv.append('-h')
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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11 args = parse_commandline()
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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12 strips = {}
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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13 for i, strip in enumerate(args.pipatterns):
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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14 strips[strip] = {'intercept': args.intercepts[i],
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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15 'fr_width': args.fr_width[i]}
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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16 with open(args.outpeptable, 'w') as fp:
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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17 for outline in annotate_peptable(args.pipeps, args.peptable,
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18 args.pepcol, args.frac_col,
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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19 args.stripcol, strips,
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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20 args.ignoremods):
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21 fp.write('\t'.join([str(x) for x in outline]))
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22 fp.write('\n')
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23
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24
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25 def get_first_matching_pattern(patterns, string):
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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26 for pattern in patterns:
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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27 if re.search(pattern, string):
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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28 return pattern
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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29 return False
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30
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31
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32 def annotate_peptable(predicted_peps_fn, peptable, seqcol, frac_col, stripcol,
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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33 strips, ignoremods):
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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34 if frac_col > 0:
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35 frac_col -= 1
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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36 predicted_peps = {}
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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37 with open(predicted_peps_fn) as fp:
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38 for line in fp:
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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39 line = line.strip('\n').split('\t')
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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40 predicted_peps[line[0]] = line[1]
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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41 not_predicted_count, predicted_count = 0, 0
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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42 with open(peptable) as fp:
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43 header = next(fp).strip('\n').split('\t')
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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44 yield header + ['Experimental pI', 'Predicted pI', 'Delta pI']
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45 for line in fp:
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46 line = line.strip('\n').split('\t')
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47 strip = strips[get_first_matching_pattern(strips.keys(),
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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48 line[stripcol - 1])]
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49 exp_pi = (strip['fr_width'] * int(line[frac_col]) +
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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50 strip['intercept'])
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51
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52 sequence = line[seqcol - 1]
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53 for weight in ignoremods:
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54 if weight == '*':
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55 regex = '[+-]\d*\.\d*'
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56 else:
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57 regex = '[+-]{}'.format(weight)
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58 sequence = re.sub(regex, '', sequence)
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59 try:
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60 pred_pi = float(predicted_peps[sequence])
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61 except KeyError:
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62 print('CANNOT PREDICT', sequence)
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63 not_predicted_count += 1
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64 pred_pi, delta_pi = 'NA', 'NA'
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65 else:
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66 delta_pi = exp_pi - pred_pi
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67 predicted_count += 1
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68 yield line + [exp_pi, pred_pi, delta_pi]
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69 print('Number of peptides without pI prediction: {}\n'
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70 'Number of peptides with predicion: {}\n'.format(not_predicted_count,
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71 predicted_count))
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72
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73
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74 def parse_commandline():
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75 parser = argparse.ArgumentParser(
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76 formatter_class=argparse.RawTextHelpFormatter)
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77 parser.add_argument('--out', dest='outpeptable', help='Output peptide '
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78 'table')
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79 parser.add_argument('-p', dest='peptable', help='Peptide/PSM table with '
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80 'peptides, FDR, fraction numbers. Used to calculate'
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81 'pI shift.')
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82 parser.add_argument('-i', dest='pipeps', help='A tab-separated txt file '
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83 'with peptide seq, pI value')
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84 parser.add_argument('--pepcol', dest='pepcol', help='Peptide sequence '
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85 'column number in peptide table. First column is 1.',
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86 default=False, type=int)
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87 parser.add_argument('--fraccol', dest='frac_col', help='Fraction number '
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88 'column number in peptide table. First column is 1.',
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89 type=int)
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90 parser.add_argument('--ignoremods', dest='ignoremods', help='Regex to '
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91 'identify modification weights to be ignored.',
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92 default=[], nargs='+', type=str)
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93 parser.add_argument('--stripcol', dest='stripcol', help='Strip name '
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94 'column number in peptide table. Will be used to '
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95 'detect strips if multiple are present using pattern '
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96 'passed with --strippatterns. First column is nr. 1.',
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97 default=False, type=int)
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98 parser.add_argument('--strippatterns', dest='pipatterns',
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99 help='Patterns to detect different pI ranges from e.g.'
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100 ' file name in peptide table', nargs='+')
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101 parser.add_argument('--intercepts', dest='intercepts',
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102 help='pI Intercept of strips', nargs='+', type=float)
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103 parser.add_argument('--widths', dest='fr_width', nargs='+',
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104 help='Strip fraction widths in pI', type=float)
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105 return parser.parse_args(sys.argv[1:])
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106
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107
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108 if __name__ == '__main__':
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109 main()