Mercurial > repos > jjohnson > spectrast

annotate link_scan_datasets.py @ 5:274fdc50169b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty
author jjohnson
date Wed, 25 Jul 2018 15:05:34 -0400
parents 7f02fc51bddf
children
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7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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1 #!/usr/bin/env python
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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2
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jjohnson
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3 from __future__ import print_function
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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jjohnson
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5 import argparse
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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6 import os
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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7 import os.path
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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8 import xml.sax
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274fdc50169b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty
jjohnson
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9 from difflib import SequenceMatcher
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12 def __main__():
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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13 parser = argparse.ArgumentParser(
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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14 description='link spectrum datasets to the name used' +
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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15 ' in the identification dataset')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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16 parser.add_argument(
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17 'ident_files', nargs='+',
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18 help='Pepxml or mzIdentML')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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19 parser.add_argument(
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20 '-n', '--scan_name', default=[], action='append',
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21 help='Name for scan file')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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22 parser.add_argument(
5
274fdc50169b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty
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23 '-f', '--scan_file', default=[], action='append',
3
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24 help='Path for scan file')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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25 args = parser.parse_args()
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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27 class MzidHandler(xml.sax.ContentHandler):
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3
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29 def __init__(self):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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30 xml.sax.ContentHandler.__init__(self)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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31 self.spectraDataFiles = []
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32 self.spectraDataNames = []
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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33 self.searchDatabaseFiles = []
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34 self.searchDatabaseNames = []
5
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35
3
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36 def startElement(self, tag, attrs):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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37 if tag == 'SpectraData':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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38 id = attrs['id']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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39 path = attrs['location']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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40 filename = os.path.basename(path)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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41 name = attrs['name'] if 'name' in attrs else None
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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42 self.spectraDataFiles.append(filename)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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43 self.spectraDataNames.append(name if name else id)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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44 print ("SpectraData: %s %s" % (name if name else id, path))
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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45 if tag == 'SearchDatabase':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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46 id = attrs['id']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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47 path = attrs['location']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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48 filename = os.path.basename(path)
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49 name = attrs['name'] if 'name' in attrs else None
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50 self.searchDatabaseFiles.append(filename)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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51 self.searchDatabaseNames.append(name if name else id)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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52 print ("SearchDatabase: %s %s" % (name if name else id, path))
5
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53
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54 def endElement(self, name):
3
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55 pass
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56
5
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57 def characters(self, data):
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58 pass
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59
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60 class PepXmlHandler(xml.sax.ContentHandler):
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61
3
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62 def __init__(self):
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63 xml.sax.ContentHandler.__init__(self)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
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64 self.spectraDataFiles = []
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65 self.spectraDataNames = []
5
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66
3
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67 def startElement(self, tag, attrs):
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68 if tag == 'msms_run_summary':
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69 basename = attrs['base_name']
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70 name = os.path.basename(basename)
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71 ext = attrs['raw_data']
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72 path = '%s%s' % (basename, ext)
3
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73 filename = os.path.basename(path)
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74 self.spectraDataFiles.append(filename)
5
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75 self.spectraDataNames.append(name)
3
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76 print ("SpectraData: %s %s" % (name, path))
5
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77
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78 def endElement(self, name):
3
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79 pass
5
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80
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81 def characters(self, data):
3
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82 pass
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83
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84 parser = xml.sax.make_parser()
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85 parser.setFeature(xml.sax.handler.feature_namespaces, 0)
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86 handler = PepXmlHandler()
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87 parser.setContentHandler(handler)
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88 for ident in args.ident_files:
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89 parser.parse(ident)
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parents:
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90
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91 spectra_names = handler.spectraDataFiles
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92
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93 def best_match(name):
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jjohnson
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94 if name in spectra_names:
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jjohnson
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95 return name
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jjohnson
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96 try:
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parents: 3
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97 r = [SequenceMatcher(None, name, spectra_names[x]).ratio()
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jjohnson
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98 for x in range(len(spectra_names))]
3
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99 return spectra_names[r.index(max(r))]
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jjohnson
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100 except Exception, e:
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101 print ("best_match: %s %s" % (name, e))
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parents:
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102
5
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jjohnson
parents: 3
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103 for i, name in enumerate(args.scan_name):
3
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jjohnson
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104 path = args.scan_file[i] if len(args.scan_file) > i else ''
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jjohnson
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105 (root, ext) = os.path.splitext(name)
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106 print ("SpectraFile: %s %s" % (name, path))
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jjohnson
parents:
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107 iname = best_match(name)
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108 print ("IdentName: %s %s" % (name, iname))
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jjohnson
parents:
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109 if not os.path.exists(iname) and os.path.exists(path):
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jjohnson
parents:
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110 os.symlink(path, iname)
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jjohnson
parents:
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111 print ("%s -> %s" % (iname, path))
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parents:
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112
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parents:
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113
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jjohnson
parents:
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114 if __name__ == "__main__":
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parents:
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115 __main__()