Mercurial > repos > iuc > reprof

annotate reprof.py @ 14:8c83f1fb30f6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit 98288bb0ee8760018924574b81c8759bac55b529
author iuc
date Fri, 11 Dec 2015 14:26:29 -0500
parents fb0936cf5bef
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
7c33ed152672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit cc30e84dcc309a93f49f75250aa3344f926cee5e-dirty
iuc
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1 #!/usr/bin/env python
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2 import re
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3 import os
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4 import argparse
7c33ed152672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit cc30e84dcc309a93f49f75250aa3344f926cee5e-dirty
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5 import subprocess
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6 import tempfile
7c33ed152672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit cc30e84dcc309a93f49f75250aa3344f926cee5e-dirty
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7 from Bio import SeqIO
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8 from BCBio import GFF
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9 from Bio.Seq import Seq
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10 from Bio.SeqRecord import SeqRecord
7c33ed152672 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit cc30e84dcc309a93f49f75250aa3344f926cee5e-dirty
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11 from Bio.SeqFeature import SeqFeature, FeatureLocation
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12
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13 def run_reprof(query_path, modeldir):
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14 outtmp = tempfile.NamedTemporaryFile(delete=False)
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15 cmd = [
1
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16 'reprof',
0
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17 '-i', query_path,
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18 '--modeldir=%s' % modeldir,
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19 '-o', outtmp.name
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20 ]
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21 subprocess.check_call(cmd)
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22 outtmp.seek(0)
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23 data = outtmp.read()
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24 outtmp.close()
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25 os.unlink(outtmp.name)
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26 return data
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27
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28 def process_reprof_report(data):
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29 KEYS = ['idx', 'AA', 'PHEL', 'RI_S', 'pH', 'pE', 'pL', 'PACC', 'PREL', 'P10', 'RI_A', 'Pbe', 'Pbie']
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30 data_tracks = {k: [] for k in KEYS}
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31
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32 for line in data.split('\n'):
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33 if line.startswith('#') or line.startswith('No') or len(line.strip()) == 0:
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34 continue
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35
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36 for idx, (key, value) in enumerate(zip(KEYS, line.strip().split('\t'))):
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37 # numerical columns
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38 if idx not in (1, 2, 11, 12):
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39 value = int(value)
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40
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41 data_tracks[key].append(value)
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42 return data_tracks
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43
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44 def storeWigData(idx, data, id, path):
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45 with open(path, 'a') as handle:
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46 handle.write('variableStep chrom=%s\n' % id)
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47 for (pos, val) in zip(idx, data):
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48 handle.write('%s %s\n' % (pos, val))
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49
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50 def storeGff3Data(path, id, positions, values, decodeMap):
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51 merged = ''.join(values)
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52 # http://stackoverflow.com/a/19683549
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53 regions = [(x[0][0].upper(), len(x[0])) for x in re.findall('((.)(\\2*))', merged)]
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54
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55 location = 1
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56
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57 rec = SeqRecord(Seq("ACTG"), id=id)
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58 for (region_char, region_length) in regions:
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59 # If we don't wish to decode this region, skip it.
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60 if region_char not in decodeMap:
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61 location += region_length
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62 continue
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63
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64 region_info = decodeMap[region_char]
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65 # Create a feature representing this region
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66 region_feat = SeqFeature(
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67 FeatureLocation(location - 1, location - 1 + region_length),
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68 type=region_info['type'], strand=0,
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69 qualifiers={k: v for (k, v) in region_info.iteritems() if k != 'type'}
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70 )
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71 # Update our start location
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72 location += region_length
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73 rec.features.append(region_feat)
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74
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75 with open(path, 'a') as handle:
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76 GFF.write([rec], handle)
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77
1
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78 def storeClassData(path, id, phel):
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79 h = float(phel.count('H')) / float(len(phel))
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80 e = float(phel.count('E')) / float(len(phel))
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81
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82 if h > .45 and e < .05:
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83 classification = 'all-alpha'
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84 elif h < .05 and e > .45:
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85 classification = 'all-beta'
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86 elif h > .3 and e > .2:
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87 classification = 'alpha-beta'
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88 else:
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89 classification = 'mixed'
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90
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91 with open(path, 'a') as handle:
7
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92 handle.write('# id\t% alpha\t% beta\tclass\n')
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93 handle.write('{0}\t{1:.2f}\t{2:.2f}\t{3}'.format(id, h, e, classification))
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94
0
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95 def main(fasta, modeldir):
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96 for record in SeqIO.parse(fasta, 'fasta'):
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97 tmp = tempfile.NamedTemporaryFile(delete=False)
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98 SeqIO.write([record], tmp, 'fasta')
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99 tmp.close()
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100
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101 # Run reprof
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102 data = process_reprof_report(run_reprof(tmp.name, modeldir))
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103 for col in ('RI_S', 'P10', 'RI_A', 'PACC', 'PREL', 'pH', 'pE', 'pL'):
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104 storeWigData(data['idx'], data[col], record.id, col + '.wig')
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105
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106 eco = ['{ECO:0000255|reprof_1.0.1}']
0
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107 storeGff3Data(
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108 'secondary_structure.gff3', record.id, data['idx'], data['PHEL'],
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109 {
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110 'H': {
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111 'type': 'peptide_helix',
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112 'description': ['Helix'],
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113 'evidence': eco,
0
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114 },
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115 'E': {
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116 'type': 'beta_strand',
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117 'description': ['Extended/Sheet'],
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118 'evidence': eco,
0
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119 },
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120 'L': {
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121 'type': 'loop',
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122 'description': ['Loop'],
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123 'evidence': eco,
0
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124 }
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125 }
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126 )
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127
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128 storeGff3Data(
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129 'solvent_accessibility.gff3', record.id, data['idx'], data['Pbe'],
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130 {
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131 'B': {
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132 'type': 'experimental_result_region',
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133 'description': ['Buried'],
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134 'evidence': eco,
0
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135 },
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136 'E': {
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137 'type': 'experimental_result_region',
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138 'description': ['Exposed'],
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139 'evidence': eco,
0
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140 },
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141 }
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142 )
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143
1
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144 storeClassData('report.tsv', record.id, data['PHEL'])
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145
0
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146
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147 if __name__ == '__main__':
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148 # Grab all of the filters from our plugin loader
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149 parser = argparse.ArgumentParser(description='Wrapper for reprof')
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150 parser.add_argument('fasta', type=file, help='Fasta Input')
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151 parser.add_argument('modeldir')
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152 args = parser.parse_args()
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153
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154 main(**vars(args))