# HG changeset patch
# User peterjc
# Date 1366210438 14400
# Node ID 8a0771c5e23618beeb000db7b202942da6cb41f2
# Parent  662fea0fe6b23cd9f9c9bb2508f9e6f8426d490b
Uploaded v0.0.5, reports number of queries with hits in stdout (peek text).

diff -r 662fea0fe6b2 -r 8a0771c5e236 tools/ncbi_blast_plus/blastxml_to_top_descr.py
--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.py	Wed Feb 20 13:36:37 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.py	Wed Apr 17 10:53:58 2013 -0400
@@ -7,6 +7,10 @@
 import sys
 import re
 
+if "-v" in sys.argv or "--version" in sys.argv:
+    print "v0.0.5"
+    sys.exit(0)
+
 if sys.version_info[:2] >= ( 2, 5 ):
     import xml.etree.cElementTree as ElementTree
 else:
@@ -58,6 +62,7 @@
 
 
 count = 0
+pos_count = 0
 outfile = open(out_file, 'w')
 outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN)))
 for event, elem in context:
@@ -103,6 +108,8 @@
             assert hit_def not in hit_descrs
             hit_descrs.append(hit_def)
         #print "%r has %i hits" % (qseqid, len(hit_descrs))
+        if hit_descrs:
+            pos_count += 1
         hit_descrs = hit_descrs[:topN]
         while len(hit_descrs) < topN:
             hit_descrs.append("")
@@ -112,4 +119,4 @@
         root.clear()
         elem.clear()
 outfile.close()
-print "%i BLAST results" % count
+print "Of %i queries, %i had BLAST results" % (count, pos_count)
diff -r 662fea0fe6b2 -r 8a0771c5e236 tools/ncbi_blast_plus/blastxml_to_top_descr.txt
--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.txt	Wed Feb 20 13:36:37 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.txt	Wed Apr 17 10:53:58 2013 -0400
@@ -52,6 +52,7 @@
          on the 'blast_datatypes' repository in the Tool Shed.
 v0.0.3 - Include the test files required to run the unit tests
 v0.0.4 - Quote filenames in case they contain spaces (internal change)
+v0.0.5 - Include number of queries with BLAST matches in stdout (peek text)
 
 
 Developers
@@ -60,7 +61,7 @@
 This script and related tools are being developed on the following hg branch:
 http://bitbucket.org/peterjc/galaxy-central/src/tools
 
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder:
 
 $ tar -czf blastxml_to_top_descr.tar.gz tools/ncbi_blast_plus/blastxml_to_top_descr.* tools/ncbi_blast_plus/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular
diff -r 662fea0fe6b2 -r 8a0771c5e236 tools/ncbi_blast_plus/blastxml_to_top_descr.xml
--- a/tools/ncbi_blast_plus/blastxml_to_top_descr.xml	Wed Feb 20 13:36:37 2013 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_top_descr.xml	Wed Apr 17 10:53:58 2013 -0400
@@ -1,5 +1,6 @@
-<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.4">
+<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.5">
     <description>Make a table from BLAST XML</description>
+    <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
     <command interpreter="python">
       blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN}
     </command>