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annotate pi_database_splitter.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 import sys
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3 import argparse
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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4 from numpy import median
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5 from contextlib import ExitStack
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6
1
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7 from peptide_pi_annotator import get_col_by_pattern
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8
0
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9
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10 def main():
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11 if sys.argv[1:] == []:
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12 sys.argv.append('-h')
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13 args = parse_commandline()
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14 locfun = {False: locatefraction,
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15 True: reverse_locatefraction}[args.reverse]
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16 # Column nrs should start from 0
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17 # If negative, -1 is last item in list, etc
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18 if args.fdrcol > 0:
1
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19 fdrcol = args.fdrcol - 1
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20 elif args.fdrcol:
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21 fdrcol = args.fdrcol
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22 elif args.fdrcolpattern:
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23 fdrcol = get_col_by_pattern(args.train_peptable, args.fdrcolpattern)
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24 else:
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25 fdrcol = False
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26 if args.deltapicol > 0:
1
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27 deltapicol = args.deltapicol - 1
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28 elif args.deltapicol:
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29 deltapicol = args.deltapicol
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30 elif args.deltapicolpattern:
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31 deltapicol = get_col_by_pattern(args.train_peptable,
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32 args.deltapicolpattern)
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33 else:
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34 deltapicol = False
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35 pishift = get_pishift(args.train_peptable, fdrcol, deltapicol,
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36 args.fdrcutoff, args.picutoff)
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37 binarray = get_bin_array(args.fr_amount, args.fr_width, args.intercept,
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38 args.tolerance, pishift)
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39 write_fractions(args.pipeps, args.fr_amount, args.prefix,
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40 binarray, locfun, args.minlen, args.maxlen)
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41
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42
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43 def locatefraction(pep_pi, bins):
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44 index = []
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45 for pibin in bins:
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46 if pep_pi > pibin[2]:
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47 continue
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48 elif pep_pi >= pibin[1]:
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49 index.append(pibin[0])
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50 else:
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51 return index
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52 return index
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53
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54
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55 def reverse_locatefraction(pep_pi, bins):
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56 index = []
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57 for pibin in bins:
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58 if pep_pi < pibin[1]:
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59 continue
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60 elif pep_pi < pibin[2]:
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61 index.append(pibin[0])
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62 else:
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63 return index
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64 return index
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65
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66
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67 def parse_commandline():
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68 parser = argparse.ArgumentParser(
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69 formatter_class=argparse.RawTextHelpFormatter)
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70 parser.add_argument('-p', dest='train_peptable', help='Peptide table with '
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71 'peptides, FDR, and fraction numbers. Used to '
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72 'calculate pI shift. Leave emtpy for no shift. '
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73 'Tab separated file.')
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74 parser.add_argument('--deltacol', dest='deltapicol', help='Delta pI column'
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75 ' number in peptide table. First column is nr. 1. '
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76 'Negative number for counting from last col '
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77 '(-1 is last).', default=False, type=int)
1
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78 parser.add_argument('--deltacolpattern', dest='deltapicolpattern',
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79 help='Delta pI column header pattern in peptide '
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80 'table.', default=False, type=str)
0
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81 parser.add_argument('--picutoff', dest='picutoff',
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82 help='delta pI value to filter experimental peptides'
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83 ' when calculating pi shift.', default=0.2, type=float)
1
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84 parser.add_argument('--fdrcolpattern', dest='fdrcolpattern',
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85 help='FDR column header pattern in peptide table.',
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86 default=False, type=str)
0
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87 parser.add_argument('--fdrcol', dest='fdrcol', help='FDR column number in '
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parents:
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88 'peptide table. First column is nr. 1. Empty includes '
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galaxyp
parents:
diff changeset
89 'all peptides', default=False, type=int)
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galaxyp
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diff changeset
90 parser.add_argument('--fdrcutoff', dest='fdrcutoff',
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galaxyp
parents:
diff changeset
91 help='FDR cutoff value to filter experimental peptides'
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galaxyp
parents:
diff changeset
92 ' when calculating pi shift.', default=0, type=float)
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93 parser.add_argument('-i', dest='pipeps', help='A tab-separated txt file '
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galaxyp
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diff changeset
94 'with accession, peptide seq, pI value')
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galaxyp
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95 parser.add_argument('--prefix', dest='prefix', default='pisep',
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96 help='Prefix for target/decoy output files')
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97 parser.add_argument('--tolerance', dest='tolerance',
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98 help='Strip fraction tolerance pi tolerance represents'
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99 ' 2.5/97.5 percentile', type=float)
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100 parser.add_argument('--amount', dest='fr_amount',
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galaxyp
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101 help='Strip fraction amount', type=int)
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102 parser.add_argument('--reverse', dest='reverse', help='Strip is reversed',
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103 action='store_const', const=True, default=False)
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104 parser.add_argument('--intercept', dest='intercept',
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105 help='pI Intercept of strip', type=float)
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106 parser.add_argument('--width', dest='fr_width',
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galaxyp
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107 help='Strip fraction width in pI', type=float)
1
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108 parser.add_argument('--minlen', dest='minlen', help='Minimal peptide length',
0
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109 type=int)
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110 parser.add_argument('--maxlen', dest='maxlen', help='Maximal peptide length',
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111 type=int, default=False)
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112 return parser.parse_args(sys.argv[1:])
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113
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114
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115 def get_pishift(peptable, fdrcol, deltapicol, fdrcutoff, delta_pi_cutoff):
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116 delta_pis = []
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117 with open(peptable) as fp:
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118 next(fp) # skip header
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119 for line in fp:
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galaxyp
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120 line = line.strip('\n').split('\t')
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121 if fdrcol:
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122 try:
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galaxyp
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123 fdr = float(line[fdrcol])
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124 except ValueError:
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125 continue
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126 if fdr > fdrcutoff:
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127 continue
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128 try:
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129 delta_pi = float(line[deltapicol])
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130 except ValueError:
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131 continue
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132 if delta_pi < delta_pi_cutoff:
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133 delta_pis.append(delta_pi)
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134 shift = median(delta_pis)
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diff changeset
135 print('pI shift (median of delta pIs): {}'.format(shift))
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136 return shift
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137
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138
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139 def get_bin_array(amount_fractions, fr_width, intercept, tolerance, pi_shift):
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140 frnr = 1
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141 bin_array = []
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galaxyp
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142 while frnr <= amount_fractions:
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galaxyp
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143 pi_center = fr_width * frnr + intercept
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galaxyp
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144 bin_left = pi_center - fr_width / 2 - tolerance - pi_shift
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galaxyp
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diff changeset
145 bin_right = pi_center + fr_width / 2 + tolerance - pi_shift
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galaxyp
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diff changeset
146 print('Bins in fraction', frnr, bin_left, bin_right)
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diff changeset
147 bin_array.append((frnr, bin_left, bin_right))
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diff changeset
148 frnr += 1
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diff changeset
149 return bin_array
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150
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151
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galaxyp
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diff changeset
152 def write_fractions(pi_peptides_fn, amount_fractions, out_prefix,
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153 bin_array, locate_function, minlen, maxlen):
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diff changeset
154 amountpad = len(str(amount_fractions))
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diff changeset
155 with ExitStack() as stack:
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galaxyp
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diff changeset
156 target_out_fp = {frnr: ([], stack.enter_context(
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galaxyp
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diff changeset
157 open('{p}_fr{i:0{pad}}.fasta'.format(p=out_prefix, i=frnr,
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diff changeset
158 pad=amountpad), 'w')))
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galaxyp
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159 for frnr in range(1, amount_fractions + 1)}
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diff changeset
160 decoy_out_fp = {frnr: ([], stack.enter_context(
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diff changeset
161 open('decoy_{p}_fr{i:0{pad}}.fasta'.format(p=out_prefix, i=frnr,
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galaxyp
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162 pad=amountpad), 'w')))
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galaxyp
parents:
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163 for frnr in range(1, amount_fractions + 1)}
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galaxyp
parents:
diff changeset
164 input_fp = stack.enter_context(open(pi_peptides_fn))
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165 pepcount = 0
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galaxyp
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166 for line in input_fp:
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galaxyp
parents:
diff changeset
167 accs, pep, pi = line.strip().split("\t")
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168 pi = float(pi)
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galaxyp
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169 if maxlen and len(pep) > maxlen:
1
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diff changeset
170 continue
0
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171 elif len(pep) >= minlen:
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172 pepcount += 1
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parents:
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173 if pep[-1] in {'K', 'R'}:
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galaxyp
parents:
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174 rev_pep = pep[::-1][1:] + pep[-1]
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175 else:
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176 rev_pep = pep[::-1]
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177 for i in locate_function(pi, bin_array):
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178 target_out_fp[i][0].append('>{}\n{}\n'.format(accs, pep))
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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179 # write pseudoReversed decoy peptide at the same time
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180 decoy_out_fp[i][0].append('>decoy_{}\n{}\n'.format(
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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181 accs, rev_pep))
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182 if pepcount > 1000000:
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183 # write in chunks to make it go faster
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184 pepcount = 0
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185 [fp.write(''.join(peps)) for peps, fp in
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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186 target_out_fp.values()]
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187 [fp.write(''.join(peps)) for peps, fp in decoy_out_fp.values()]
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188 target_out_fp = {fr: ([], pep_fp[1])
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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189 for fr, pep_fp in target_out_fp.items()}
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190 decoy_out_fp = {fr: ([], pep_fp[1])
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191 for fr, pep_fp in decoy_out_fp.items()}
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192 [fp.write(''.join(peps)) for peps, fp in target_out_fp.values()]
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193 [fp.write(''.join(peps)) for peps, fp in decoy_out_fp.values()]
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194
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195
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196 if __name__ == '__main__':
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197 main()