diff idxml_exporter.py @ 0:ba86fd127f5a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idxml_exporter.py	Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,68 @@
+from xml.sax import make_parser, ContentHandler
+from optparse import OptionParser
+
+
+def main():
+    (options, _) = _parse_args()
+    with open(options.output, "w") as out:
+        parser = make_parser()
+        handler = _get_handler(options, out)
+        parser.setContentHandler(handler)
+        parser.parse(open(options.input, "r"))
+
+
+def _get_handler(option, out):
+    return PeptideHandler(out)
+
+
+class PeptideHandler(ContentHandler):
+    record_values = {
+        "IdentificationRun": ["search_engine"],
+        "PeptideIdentification": ["score_type", "significance_threshold", "MZ", "RT"],
+        "PeptideHit": ["score", "sequence", "charge"],
+    }
+
+    def __init__(self, output):
+        self.output = output
+
+    def __record_values(self, keys, attrs):
+        for key in keys:
+            setattr(self, key, attrs.get(key, None))
+
+    def startElement(self, name, attrs):
+        self._set_attributes(name, attrs)
+
+    def endElement(self, name):
+        if name == "PeptideHit":
+            self._write_peptide()
+        # reset values for element
+        self._set_attributes(name, {})
+
+    def _write_peptide(self):
+        col_keys = ["score", "peptide", "score_type", "charge", "MZ", "RT"]
+        row_values = self._get_values(col_keys)
+        row = "\t".join(row_values)
+        self._write_line(row)
+
+    def _write_line(self, line):
+        self.output.write(line)
+        self.output.write("\n")
+
+    def _get_values(self, keys):
+        return [getattr(self, key, "") for key in keys]
+
+    def _set_attributes(self, name, attrs):
+        for element_name, element_attributes in self.record_values.iteritems():
+            if name == element_name:
+                self.__record_values(element_attributes, attrs)
+
+
+def _parse_args():
+    parser = OptionParser()
+    parser.add_option("--input", dest="input")
+    parser.add_option("--output", dest="output")
+    parser.add_option("--type", dest="type", choices=["peptide"])
+    return parser.parse_args()
+
+if __name__ == "__main__":
+    main()