diff megablast_xml_parser.py @ 1:3ce5d56297ed draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser commit 3ccddd4e2032535ead030efa401e690ffb80d145"

--- a/megablast_xml_parser.py	Mon May 19 10:59:33 2014 -0400
+++ b/megablast_xml_parser.py	Wed Sep 09 10:27:20 2020 +0000
@@ -1,78 +1,64 @@
 #!/usr/bin/env python
-    
-import sys, os, re
 
-if sys.version_info[:2] >= ( 2, 5 ):
-    import xml.etree.cElementTree as ElementTree
-else:
-    from galaxy import eggs
-    import pkg_resources; pkg_resources.require( "elementtree" )
-    from elementtree import ElementTree
+import re
+import sys
+import xml.etree.cElementTree as ElementTree
 
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
-    sys.exit()
 
 def __main__():
-    source  = sys.argv[1]
-    hspTags = [
-           "Hsp_bit-score",
-           "Hsp_evalue",
-           "Hsp_query-from",
-           "Hsp_query-to",
-           "Hsp_hit-from",
-           "Hsp_hit-to",
-           "Hsp_query-frame",
-           "Hsp_hit-frame",
-           "Hsp_identity",
-           "Hsp_align-len",
-           "Hsp_qseq",
-           "Hsp_hseq",
-           "Hsp_midline"
-          ]
-    hspData = []
+    source = sys.argv[1]
+    hspTags = ["Hsp_bit-score",
+               "Hsp_evalue",
+               "Hsp_query-from",
+               "Hsp_query-to",
+               "Hsp_hit-from",
+               "Hsp_hit-to",
+               "Hsp_query-frame",
+               "Hsp_hit-frame",
+               "Hsp_identity",
+               "Hsp_align-len",
+               "Hsp_qseq",
+               "Hsp_hseq",
+               "Hsp_midline"]
 
     # get an iterable
-    try: 
-        context = ElementTree.iterparse( source, events=( "start", "end" ) )
-    except:
-        stop_err( "Invalid data format." )
+    try:
+        context = ElementTree.iterparse(source, events=("start", "end"))
+    except Exception:
+        sys.exit("Invalid data format.")
     # turn it into an iterator
-    context = iter( context )
+    context = iter(context)
     # get the root element
     try:
-        event, root = context.next()
-    except:
-        stop_err( "Invalid data format." )
+        event, root = next(context)
+    except Exception:
+        sys.exit("Invalid data format.")
 
-    outfile = open( sys.argv[2], 'w' )
-    try:
-        for event, elem in context:
-           # for every <Iteration> tag
-           if event == "end" and elem.tag == "Iteration":
-               query = elem.findtext( "Iteration_query-def" )
-               qLen = elem.findtext( "Iteration_query-len" )
-               # for every <Hit> within <Iteration>
-               for hit in elem.findall( "Iteration_hits/Hit" ):
-                   subject = hit.findtext( "Hit_id" )
-                   if re.search( '^gi', subject ):
-                       subject = subject.split('|')[1]
-                   sLen = hit.findtext( "Hit_len" )
-                   # for every <Hsp> within <Hit>
-                   for hsp in hit.findall( "Hit_hsps/Hsp" ):
-                        outfile.write( "%s\t%s\t%s\t%s" % ( query, qLen, subject, sLen ) )
-                        for tag in hspTags:
-                            outfile.write("\t%s" %(hsp.findtext( tag )))
-                            #hspData.append( hsp.findtext( tag ) )
-                        #hspData = []
-                        outfile.write('\n')
-               # prevents ElementTree from growing large datastructure
-               root.clear()
-               elem.clear()
-    except:
-        outfile.close()
-        stop_err( "The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1] )
+    with open(sys.argv[2], 'w') as outfile:
+        try:
+            for event, elem in context:
+                # for every <Iteration> tag
+                if event == "end" and elem.tag == "Iteration":
+                    query = elem.findtext("Iteration_query-def")
+                    qLen = elem.findtext("Iteration_query-len")
+                    # for every <Hit> within <Iteration>
+                    for hit in elem.findall("Iteration_hits/Hit"):
+                        subject = hit.findtext("Hit_id")
+                        if re.search('^gi', subject):
+                            subject = subject.split('|')[1]
+                        sLen = hit.findtext("Hit_len")
+                        # for every <Hsp> within <Hit>
+                        for hsp in hit.findall("Hit_hsps/Hsp"):
+                            outfile.write("%s\t%s\t%s\t%s" % (query, qLen, subject, sLen))
+                            for tag in hspTags:
+                                outfile.write("\t%s" % (hsp.findtext(tag)))
+                            outfile.write('\n')
+                    # prevents ElementTree from growing large datastructure
+                    root.clear()
+                    elem.clear()
+        except Exception:
+            sys.exit("The input data is malformed, or there is more than one dataset in the input file. Error: %s" % sys.exc_info()[1])
 
-    outfile.close()
 
-if __name__ == "__main__": __main__()
+if __name__ == "__main__":
+    __main__()