Mercurial > repos > galaxyp > hirieftools

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

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit decb06dc90d7069d317968b979f649a04720b264
author galaxyp
date Thu, 14 Sep 2017 11:55:02 -0400
parents 8a30d6e5b97d
children
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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
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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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
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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():
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9 if sys.argv[1:] == []:
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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()
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12 strips = {}
1
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13 if args.frac_col > 0:
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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14 frac_col = args.frac_col - 1
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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15 elif args.frac_col:
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16 frac_col = args.frac_col
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17 elif args.frac_colpattern:
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18 frac_col = get_col_by_pattern(args.peptable, args.frac_colpattern)
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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19 else:
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20 raise RuntimeError('Must define fraction column')
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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21 if args.stripcol > 0:
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22 stripcol = args.stripcol - 1
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23 elif args.stripcol:
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24 stripcol = args.stripcol
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25 elif args.stripcolpattern:
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26 stripcol = get_col_by_pattern(args.peptable, args.stripcolpattern)
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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27 else:
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28 raise RuntimeError('Must define strip column')
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29 if args.pepcol:
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30 pepcol = args.pepcol - 1
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31 elif args.pepcolpattern:
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32 pepcol = get_col_by_pattern(args.peptable, args.pepcolpattern)
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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33 else:
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34 raise RuntimeError('Must define peptide sequence column')
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35 for i, strip in enumerate(args.pipatterns):
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36 strips[strip] = {'intercept': args.intercepts[i],
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37 'fr_width': args.fr_width[i]}
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38 with open(args.outpeptable, 'w') as fp:
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39 for outline in annotate_peptable(args.pipeps, args.peptable, pepcol,
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40 frac_col, stripcol, strips,
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41 args.ignoremods):
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42 fp.write('\t'.join([str(x) for x in outline]))
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43 fp.write('\n')
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44
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45
3
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46 def get_strip(strips, string):
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47 for pattern in strips.keys():
0
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48 if re.search(pattern, string):
3
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49 return strips[pattern]
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50 return False
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51
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52
1
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53 def get_col_by_pattern(peptable, colpattern):
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54 with open(peptable) as fp:
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55 header = next(fp).strip('\n').split('\t')
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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56 for ix, field in enumerate(header):
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57 if colpattern in field:
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58 return ix
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59
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60
0
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61 def annotate_peptable(predicted_peps_fn, peptable, seqcol, frac_col, stripcol,
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62 strips, ignoremods):
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63 predicted_peps = {}
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64 with open(predicted_peps_fn) as fp:
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65 for line in fp:
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66 line = line.strip('\n').split('\t')
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67 predicted_peps[line[0]] = line[1]
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68 not_predicted_count, predicted_count = 0, 0
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69 with open(peptable) as fp:
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70 header = next(fp).strip('\n').split('\t')
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71 yield header + ['Experimental pI', 'Predicted pI', 'Delta pI']
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72 for line in fp:
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73 line = line.strip('\n').split('\t')
1
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74 sequence = line[seqcol]
0
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75 for weight in ignoremods:
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76 if weight == '*':
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77 regex = '[+-]\d*\.\d*'
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78 else:
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79 regex = '[+-]{}'.format(weight)
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80 sequence = re.sub(regex, '', sequence)
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81 try:
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82 pred_pi = float(predicted_peps[sequence])
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83 except KeyError:
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84 print('CANNOT PREDICT', sequence)
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85 not_predicted_count += 1
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86 pred_pi, delta_pi = 'NA', 'NA'
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87 else:
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88 predicted_count += 1
3
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89 strip = get_strip(strips, line[stripcol])
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90 if not strip:
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91 exp_pi, delta_pi = 'NA', 'NA'
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92 else:
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93 try:
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94 exp_pi = (strip['fr_width'] * int(line[frac_col]) +
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95 strip['intercept'])
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96 except ValueError:
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97 print('Cannot detect fraction for PSM {}'.format(sequence))
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98 exp_pi, delta_pi = 'NA', 'NA'
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99 else:
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100 if pred_pi != 'NA':
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101 delta_pi = exp_pi - pred_pi
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102 else:
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103 delta_pi = 'NA'
0
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104 yield line + [exp_pi, pred_pi, delta_pi]
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105 print('Number of peptides without pI prediction: {}\n'
3
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106 'Number of peptides predicted: {}\n'.format(not_predicted_count,
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107 predicted_count))
0
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108
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109
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110 def parse_commandline():
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111 parser = argparse.ArgumentParser(
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112 formatter_class=argparse.RawTextHelpFormatter)
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113 parser.add_argument('--out', dest='outpeptable', help='Output peptide '
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114 'table')
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115 parser.add_argument('-p', dest='peptable', help='Peptide/PSM table with '
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116 'peptides, FDR, fraction numbers. Used to calculate'
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117 'pI shift.')
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118 parser.add_argument('-i', dest='pipeps', help='A tab-separated txt file '
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119 'with peptide seq, pI value')
1
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120 parser.add_argument('--pepcolpattern', dest='pepcolpattern',
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121 help='Peptide sequence column pattern in peptide '
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122 'table.', default=False, type=str)
0
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123 parser.add_argument('--pepcol', dest='pepcol', help='Peptide sequence '
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124 'column number in peptide table. First column is 1.',
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125 default=False, type=int)
1
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126 parser.add_argument('--fraccolpattern', dest='frac_colpattern',
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127 help='Fraction number column pattern in peptide '
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128 'table.', default=False, type=str)
0
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129 parser.add_argument('--fraccol', dest='frac_col', help='Fraction number '
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130 'column number in peptide table. First column is 1.',
1
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131 default=False, type=int)
0
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132 parser.add_argument('--ignoremods', dest='ignoremods', help='Regex to '
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133 'identify modification weights to be ignored.',
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134 default=[], nargs='+', type=str)
1
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135 parser.add_argument('--stripcolpattern', dest='stripcolpattern',
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136 help='Strip name column pattern in peptide '
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137 'table.', type=str, default=False)
0
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138 parser.add_argument('--stripcol', dest='stripcol', help='Strip name '
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139 'column number in peptide table. Will be used to '
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140 'detect strips if multiple are present using pattern '
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141 'passed with --strippatterns. First column is nr. 1.',
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142 default=False, type=int)
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143 parser.add_argument('--strippatterns', dest='pipatterns',
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144 help='Patterns to detect different pI ranges from e.g.'
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145 ' file name in peptide table', nargs='+')
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146 parser.add_argument('--intercepts', dest='intercepts',
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147 help='pI Intercept of strips', nargs='+', type=float)
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148 parser.add_argument('--widths', dest='fr_width', nargs='+',
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149 help='Strip fraction widths in pI', type=float)
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150 return parser.parse_args(sys.argv[1:])
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151
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152
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153 if __name__ == '__main__':
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154 main()