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comparison idxml_exporter.py @ 0:ba86fd127f5a draft

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author galaxyp
date Wed, 19 Dec 2012 00:32:25 -0500
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-1:000000000000 0:ba86fd127f5a
1 from xml.sax import make_parser, ContentHandler
2 from optparse import OptionParser
3
4
5 def main():
6 (options, _) = _parse_args()
7 with open(options.output, "w") as out:
8 parser = make_parser()
9 handler = _get_handler(options, out)
10 parser.setContentHandler(handler)
11 parser.parse(open(options.input, "r"))
12
13
14 def _get_handler(option, out):
15 return PeptideHandler(out)
16
17
18 class PeptideHandler(ContentHandler):
19 record_values = {
20 "IdentificationRun": ["search_engine"],
21 "PeptideIdentification": ["score_type", "significance_threshold", "MZ", "RT"],
22 "PeptideHit": ["score", "sequence", "charge"],
23 }
24
25 def __init__(self, output):
26 self.output = output
27
28 def __record_values(self, keys, attrs):
29 for key in keys:
30 setattr(self, key, attrs.get(key, None))
31
32 def startElement(self, name, attrs):
33 self._set_attributes(name, attrs)
34
35 def endElement(self, name):
36 if name == "PeptideHit":
37 self._write_peptide()
38 # reset values for element
39 self._set_attributes(name, {})
40
41 def _write_peptide(self):
42 col_keys = ["score", "peptide", "score_type", "charge", "MZ", "RT"]
43 row_values = self._get_values(col_keys)
44 row = "\t".join(row_values)
45 self._write_line(row)
46
47 def _write_line(self, line):
48 self.output.write(line)
49 self.output.write("\n")
50
51 def _get_values(self, keys):
52 return [getattr(self, key, "") for key in keys]
53
54 def _set_attributes(self, name, attrs):
55 for element_name, element_attributes in self.record_values.iteritems():
56 if name == element_name:
57 self.__record_values(element_attributes, attrs)
58
59
60 def _parse_args():
61 parser = OptionParser()
62 parser.add_option("--input", dest="input")
63 parser.add_option("--output", dest="output")
64 parser.add_option("--type", dest="type", choices=["peptide"])
65 return parser.parse_args()
66
67 if __name__ == "__main__":
68 main()