Mercurial > repos > peterjc > blastxml_to_top_descr
changeset 16:6ade4e7c63b3 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr commit 96d587fc6f6cab23c597e88a83daf7eecd0d4162-dirty
| author | peterjc |
|---|---|
| date | Thu, 09 Feb 2017 11:22:39 -0500 |
| parents | 60d0c6c1a71f |
| children | ccf0a59e8537 |
| files | tools/blastxml_to_top_descr/blastxml_to_top_descr.py tools/blastxml_to_top_descr/repository_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Fri Feb 03 12:38:33 2017 -0500 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Thu Feb 09 11:22:39 2017 -0500 @@ -6,9 +6,11 @@ Assumes the hits are pre-sorted, so "best" 3 hits gives first 3 hits. """ + import os +import re import sys -import re + from optparse import OptionParser if "-v" in sys.argv or "--version" in sys.argv: @@ -18,7 +20,7 @@ if sys.version_info[:2] >= (2, 5): import xml.etree.cElementTree as ElementTree else: - from galaxy import eggs + from galaxy import eggs # noqa - ignore flake8 F401 import pkg_resources pkg_resources.require("elementtree") from elementtree import ElementTree @@ -221,6 +223,7 @@ # Final query yield current_query, hit_descrs + if options.format == "blastxml": hits = blastxml_hits(in_file) elif options.format == "tabular": @@ -238,6 +241,7 @@ else: return descriptions[:topN] + count = 0 if out_file is None: outfile = sys.stdout
--- a/tools/blastxml_to_top_descr/repository_dependencies.xml Fri Feb 03 12:38:33 2017 -0500 +++ b/tools/blastxml_to_top_descr/repository_dependencies.xml Thu Feb 09 11:22:39 2017 -0500 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Requires BLAST XML and database datatype definitions."> -<repository changeset_revision="623a3fbe5340" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +<repository changeset_revision="310ec0f47485" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>