2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1131b031cec7/ changeset: 1131b031cec7 user: natefoo date: 2011-06-09 17:22:23 summary: Fix for either a bug or undocumented feature in ElementTree that broke megablast and blast+ XML parsing in Python 2.7. affected #: 2 files (2 bytes) --- a/tools/metag_tools/megablast_xml_parser.py Wed Jun 08 23:50:07 2011 -0400 +++ b/tools/metag_tools/megablast_xml_parser.py Thu Jun 09 11:22:23 2011 -0400 @@ -53,7 +53,7 @@ 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/" ): + for hit in elem.findall( "Iteration_hits/Hit" ): subject = hit.findtext( "Hit_id" ) if re.search( '^gi', subject ): subject = subject.split('|')[1] --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Wed Jun 08 23:50:07 2011 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Jun 09 11:22:23 2011 -0400 @@ -138,7 +138,7 @@ qlen = int(elem.findtext("Iteration_query-len")) # for every <Hit> within <Iteration> - for hit in elem.findall("Iteration_hits/Hit/"): + for hit in elem.findall("Iteration_hits/Hit"): #Expecting either this, # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> # <Hit_def>RecName: Full=Rhodopsin</Hit_def> http://bitbucket.org/galaxy/galaxy-central/changeset/d394deb322a9/ changeset: d394deb322a9 user: natefoo date: 2011-06-09 17:24:19 summary: Rebuild the bx_python egg for numpy 1.6.0. Python 2.7 support officially in beta (tests are passing nicely). affected #: 1 file (9 bytes) --- a/eggs.ini Thu Jun 09 11:22:23 2011 -0400 +++ b/eggs.ini Thu Jun 09 11:24:19 2011 -0400 @@ -67,7 +67,7 @@ psycopg2 = _8.4.2_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _494c2d1d68b3 +bx_python = _494c2d1d68b3_rebuild1 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 pysam = _kanwei_b10f6e722e9a Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.