diff link_scan_datasets.py @ 3:7f02fc51bddf draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit 379705f578f9a0465f497894c7d2b5f68b6a55e6-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/link_scan_datasets.py	Wed Jul 25 10:58:17 2018 -0400
@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import difflib
+from difflib import SequenceMatcher
+import os
+import os.path
+import sys
+import xml.sax
+
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='link spectrum datasets to the name used' +
+                    ' in the identification dataset')
+    parser.add_argument(
+        'ident_files', nargs='+', 
+        help='Pepxml or mzIdentML')
+    parser.add_argument(
+        '-n', '--scan_name', default=[], action='append', 
+        help='Name for scan file')
+    parser.add_argument(
+        '-f', '--scan_file', default=[], action='append', 
+        help='Path for scan file')
+    args = parser.parse_args()
+
+    class MzidHandler( xml.sax.ContentHandler):
+        def __init__(self):
+            xml.sax.ContentHandler.__init__(self)
+            self.spectraDataFiles = []
+            self.spectraDataNames = []
+            self.searchDatabaseFiles = []
+            self.searchDatabaseNames = []
+        def startElement(self, tag, attrs):
+            if tag == 'SpectraData':
+                id = attrs['id']
+                path = attrs['location']
+                filename = os.path.basename(path)
+                name = attrs['name'] if 'name' in attrs else None
+                self.spectraDataFiles.append(filename)
+                self.spectraDataNames.append(name if name else id)
+                print ("SpectraData: %s  %s" % (name if name else id, path))
+            if tag == 'SearchDatabase':
+                id = attrs['id']
+                path = attrs['location']
+                filename = os.path.basename(path)
+                name = attrs['name'] if 'name' in attrs else None
+                self.searchDatabaseFiles.append(filename)
+                self.searchDatabaseNames.append(name if name else id)
+                print ("SearchDatabase: %s  %s" % (name if name else id, path))
+        def endElement( self, name):
+            pass
+        def characters( self, data):
+            pass
+
+    class PepXmlHandler( xml.sax.ContentHandler):
+        def __init__(self):
+            xml.sax.ContentHandler.__init__(self)
+            self.spectraDataFiles = []
+            self.spectraDataNames = []
+        def startElement(self, tag, attrs):
+            if tag == 'msms_run_summary':
+                basename = attrs['base_name']
+                name = os.path.basename(basename)
+                ext = attrs['raw_data']
+                path = '%s%s' % (basename,ext)
+                filename = os.path.basename(path)
+                self.spectraDataFiles.append(filename)
+                self.spectraDataNames.append(name) 
+                print ("SpectraData: %s  %s" % (name, path))
+        def endElement( self, name):
+            pass
+        def characters( self, data):
+            pass
+
+    parser = xml.sax.make_parser()
+    parser.setFeature(xml.sax.handler.feature_namespaces, 0)
+    handler = PepXmlHandler()
+    parser.setContentHandler( handler )
+    for ident in args.ident_files:
+        parser.parse(ident)
+
+    spectra_names = handler.spectraDataFiles
+
+    def best_match(name):
+        if name in spectra_names:
+            return name
+        try:
+            r = [SequenceMatcher(None, name, spectra_names[x]).ratio() for x in range(len(spectra_names))]
+            return spectra_names[r.index(max(r))]
+        except Exception, e:
+            print ("best_match: %s  %s" % (name, e))
+
+    for i,name in enumerate(args.scan_name):
+        path = args.scan_file[i] if len(args.scan_file) > i else ''
+        (root, ext) = os.path.splitext(name)
+        print ("SpectraFile: %s  %s" % (name, path))
+        iname = best_match(name)
+        print ("IdentName: %s  %s" % (name, iname))
+        if not os.path.exists(iname) and os.path.exists(path):
+            os.symlink(path, iname)
+            print ("%s -> %s" % (iname, path))
+
+
+if __name__ == "__main__":
+    __main__()
+