Mercurial > repos > jjohnson > spectrast

annotate link_scan_datasets.py @ 3:7f02fc51bddf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
author jjohnson
date Wed, 25 Jul 2018 10:58:17 -0400
parents
children 274fdc50169b
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3
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
diff changeset
1 #!/usr/bin/env python
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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2
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
diff changeset
3 from __future__ import print_function
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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4
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
diff changeset
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 difflib
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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7 from difflib import SequenceMatcher
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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diff changeset
8 import os
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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9 import os.path
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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10 import sys
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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11 import xml.sax
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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12
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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13
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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14
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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15 def __main__():
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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16 parser = argparse.ArgumentParser(
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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17 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
jjohnson
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18 ' in the identification dataset')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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19 parser.add_argument(
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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20 'ident_files', nargs='+',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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21 help='Pepxml or mzIdentML')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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22 parser.add_argument(
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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23 '-n', '--scan_name', default=[], action='append',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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24 help='Name for scan file')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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25 parser.add_argument(
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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26 '-f', '--scan_file', default=[], action='append',
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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27 help='Path for scan file')
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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28 args = parser.parse_args()
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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29
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jjohnson
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30 class MzidHandler( xml.sax.ContentHandler):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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31 def __init__(self):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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32 xml.sax.ContentHandler.__init__(self)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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33 self.spectraDataFiles = []
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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34 self.spectraDataNames = []
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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35 self.searchDatabaseFiles = []
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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36 self.searchDatabaseNames = []
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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37 def startElement(self, tag, attrs):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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38 if tag == 'SpectraData':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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39 id = attrs['id']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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40 path = attrs['location']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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41 filename = os.path.basename(path)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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42 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
jjohnson
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43 self.spectraDataFiles.append(filename)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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44 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
jjohnson
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45 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
jjohnson
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46 if tag == 'SearchDatabase':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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47 id = attrs['id']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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48 path = attrs['location']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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49 filename = os.path.basename(path)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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50 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
jjohnson
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51 self.searchDatabaseFiles.append(filename)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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52 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
jjohnson
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53 print ("SearchDatabase: %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
jjohnson
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54 def endElement( self, name):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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55 pass
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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56 def characters( self, data):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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57 pass
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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58
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jjohnson
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59 class PepXmlHandler( xml.sax.ContentHandler):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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60 def __init__(self):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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61 xml.sax.ContentHandler.__init__(self)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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62 self.spectraDataFiles = []
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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63 self.spectraDataNames = []
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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64 def startElement(self, tag, attrs):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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65 if tag == 'msms_run_summary':
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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66 basename = attrs['base_name']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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67 name = os.path.basename(basename)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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68 ext = attrs['raw_data']
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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69 path = '%s%s' % (basename,ext)
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jjohnson
parents:
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70 filename = os.path.basename(path)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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71 self.spectraDataFiles.append(filename)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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72 self.spectraDataNames.append(name)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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73 print ("SpectraData: %s %s" % (name, path))
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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74 def endElement( self, name):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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75 pass
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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76 def characters( self, data):
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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77 pass
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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78
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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79 parser = xml.sax.make_parser()
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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80 parser.setFeature(xml.sax.handler.feature_namespaces, 0)
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
parents:
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81 handler = PepXmlHandler()
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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82 parser.setContentHandler( handler )
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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83 for ident in args.ident_files:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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84 parser.parse(ident)
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85
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jjohnson
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86 spectra_names = handler.spectraDataFiles
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87
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jjohnson
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88 def best_match(name):
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jjohnson
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89 if name in spectra_names:
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jjohnson
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90 return name
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jjohnson
parents:
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91 try:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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92 r = [SequenceMatcher(None, name, spectra_names[x]).ratio() for x in range(len(spectra_names))]
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jjohnson
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93 return spectra_names[r.index(max(r))]
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jjohnson
parents:
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94 except Exception, e:
7f02fc51bddf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty
jjohnson
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95 print ("best_match: %s %s" % (name, e))
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jjohnson
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96
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jjohnson
parents:
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97 for i,name in enumerate(args.scan_name):
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jjohnson
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98 path = args.scan_file[i] if len(args.scan_file) > i else ''
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jjohnson
parents:
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99 (root, ext) = os.path.splitext(name)
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jjohnson
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100 print ("SpectraFile: %s %s" % (name, path))
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jjohnson
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101 iname = best_match(name)
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jjohnson
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102 print ("IdentName: %s %s" % (name, iname))
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jjohnson
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103 if not os.path.exists(iname) and os.path.exists(path):
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jjohnson
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104 os.symlink(path, iname)
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jjohnson
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105 print ("%s -> %s" % (iname, path))
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jjohnson
parents:
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106
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107
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jjohnson
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108 if __name__ == "__main__":
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jjohnson
parents:
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109 __main__()
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jjohnson
parents:
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110