[galaxy-dev] [hg] galaxy 3425: Bug fixes to LCA tool

24 Feb 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/c0192e97a79a
changeset: 3425:c0192e97a79a
user:      gua110
date:      Mon Feb 22 16:22:12 2010 -0500
description:
Bug fixes to LCA tool
diffstat:
test-data/lca_input2.taxonomy  |    4 +
 test-data/lca_input3.taxonomy  |  100 +++++++++++++++++++++++++++++++++++++++++
 test-data/lca_output2.taxonomy |    1 +
 test-data/lca_output3.taxonomy |   40 ++++++++++++++++
 tools/taxonomy/lca.py          |   49 +++++++++++++------
 tools/taxonomy/lca.xml         |   24 +++++++--
 6 files changed, 195 insertions(+), 23 deletions(-)
diffs (308 lines):
diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_input2.taxonomy

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_input2.taxonomy	Mon Feb 22 16:22:12 2010 -0500
@@ -0,0 +1,4 @@
+read_1	1	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	genus1	subgenus1	species1	subspecies1	1	2	3	4
+read_1	2	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	genus2	subgenus2	species2	subspecies2	1	2	3	4
+read_2	3	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum3	subphylum3	superclass3	class3	subclass3	superorder3	order3	suborder3	superfamily3	family3	subfamily3	tribe3	subtribe3	genus3	subgenus3	species3	subspecies3	1	X	Y	Z
+read_2	4	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum4	subphylum4	superclass4	class4	subclass4	superorder4	order4	suborder4	superfamily4	family4	subfamily4	tribe4	subtribe4	genus4	subgenus4	species4	subspecies4	1	X	Y	Z
diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_input3.taxonomy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_input3.taxonomy	Mon Feb 22 16:22:12 2010 -0500
@@ -0,0 +1,100 @@
+IA_1-79371	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-84488	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-270826	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-285361	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-93958	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-99821	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-144417	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-278966	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-314709	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-324951	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-27817	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604153
+IA_1-95255	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604181
+IA_1-104173	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-135979	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-139090	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-139090	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-139090	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-144996	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-161439	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-216231	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-237681	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-250166	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-254274	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-254274	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-27817	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-29000	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-291427	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-291427	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-293054	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-293054	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-296315	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-296315	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus
+IA_1-310974	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-310974	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-311282	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-311282	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-322295	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n
+IA_1-42600	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-45102	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-45102	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-48105	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-48105	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-57254	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-61975	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-61975	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-66943	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-68288	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-82334	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-95526	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_output2.taxonomy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_output2.taxonomy	Mon Feb 22 16:22:12 2010 -0500
@@ -0,0 +1,1 @@
+read_1	1	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	n	n	n	n	1	2	3	4
diff -r 9d9f0dfeeebf -r c0192e97a79a test-data/lca_output3.taxonomy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_output3.taxonomy	Mon Feb 22 16:22:12 2010 -0500
@@ -0,0 +1,40 @@
+IA_1-104173	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-135979	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-139090	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-144417	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-144996	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-161439	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-216231	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-237681	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-250166	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-254274	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-270826	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-27817	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604153
+IA_1-278966	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-285361	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-29000	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-291427	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-293054	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-296315	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-310974	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-311282	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-314709	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-324951	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-42600	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-45102	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-48105	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-57254	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-61975	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-66943	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-68288	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-79371	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-82334	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-84488	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-93958	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-95255	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604181
+IA_1-95526	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-99821	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
diff -r 9d9f0dfeeebf -r c0192e97a79a tools/taxonomy/lca.py
--- a/tools/taxonomy/lca.py	Mon Feb 22 13:56:51 2010 -0500
+++ b/tools/taxonomy/lca.py	Mon Feb 22 16:22:12 2010 -0500
@@ -42,6 +42,16 @@
     except:
         stop_err("Syntax error: Use correct syntax: program infile outfile")
+    fin = open(sys.argv[1],'r')
+    for j, line in enumerate( fin ):
+        elems = line.strip().split('\t')
+        if len(elems) < 24:
+            stop_err("The format of the input dataset is incorrect. Taxonomy datatype should contain at least 24 columns.")
+        if j > 30:
+            break
+        cols = range(1,len(elems))
+    fin.close()
+       
     group_col = 0
     tmpfile = tempfile.NamedTemporaryFile()
@@ -68,11 +78,11 @@
     remaining_vals = []
     skipped_lines = 0
     fout = open(outfile, "w")
-    cols = range(1,25)
     block_valid = False
+    
     for ii, line in enumerate( file( tmpfile.name )):
-        if line and not line.startswith( '#' ):
+        if line and not line.startswith( '#' ) and len(line.split('\t')) >= 24: #Taxonomy datatype should have at least 24 columns
             line = line.rstrip( '\r\n' )
             try:
                 fields = line.split("\t")
@@ -95,14 +105,11 @@
                         corresponding aggregate values into the output file.  This works 
                         due to the sort on group_col we've applied to the data above.
                         """
-                        out_list = ['']*25
+                        out_list = ['']*24
                         out_list[0] = str(prev_item)
                         out_list[1] = str(prev_vals[0][0])
                         out_list[2] = str(prev_vals[1][0])
-                        try:
-                            out_list[24] = str(prev_vals[23][0])
-                        except:
-                            pass
+                        
                         for k, col in enumerate(cols):
                             if col >= 3 and col < 24:
                                 if len(set(prev_vals[k])) == 1:
@@ -113,11 +120,17 @@
                             out_list[k+1] = 'n' 
                             k += 1
+                        j = 0
+                        while True:
+                            try:
+                                out_list.append(str(prev_vals[23+j][0]))
+                                j += 1
+                            except:
+                                break
+                            
                         if rank_bound == 0:     
                             print >>fout, '\t'.join(out_list).strip()
-                            #print 'n'*( 24 - rank_bound )
                         else:
-                            #print '\t'.join(out_list[rank_bound:24])
                             if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
                                 print >>fout, '\t'.join(out_list).strip()
@@ -144,15 +157,11 @@
             skipped_lines += 1
# Handle the last grouped value
-    out_list = ['']*25
+    out_list = ['']*24
     out_list[0] = str(prev_item)
     out_list[1] = str(prev_vals[0][0])
     out_list[2] = str(prev_vals[1][0])
-    try:
-        out_list[24] = str(prev_vals[23][0])
-    except:
-        pass
-
+    
     for k, col in enumerate(cols):
         if col >= 3 and col < 24:
             if len(set(prev_vals[k])) == 1:
@@ -163,11 +172,17 @@
         out_list[k+1] = 'n' 
         k += 1
+    j = 0
+    while True:
+        try:
+            out_list.append(str(prev_vals[23+j][0]))
+            j += 1
+        except:
+            break
+        
     if rank_bound == 0:     
         print >>fout, '\t'.join(out_list).strip()
     else:
-        #print ''.join(out_list[rank_bound:24])
-        #print 'n'*( 24 - rank_bound )
         if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
             print >>fout, '\t'.join(out_list).strip()
diff -r 9d9f0dfeeebf -r c0192e97a79a tools/taxonomy/lca.xml
--- a/tools/taxonomy/lca.xml	Mon Feb 22 13:56:51 2010 -0500
+++ b/tools/taxonomy/lca.xml	Mon Feb 22 16:22:12 2010 -0500
@@ -1,4 +1,4 @@
-<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.0">
+<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
   <description></description>
   <command interpreter="python">
     lca.py $input1 $out_file1 $rank_bound
@@ -34,11 +34,23 @@
     <data format="taxonomy" name="out_file1" metadata_source="input1" />
   </outputs>
   <tests>
- <test>
-      <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
-      <param name="rank_bound" value="0" />
-      <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
- </test> 
+     <test>
+          <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
+          <param name="rank_bound" value="0" />
+          <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
+     </test> 
+     <test>
+          <param name="input1" value="lca_input2.taxonomy" ftype="taxonomy"/>
+          <param name="rank_bound" value="7" />
+          <output name="out_file1" file="lca_output2.taxonomy" ftype="taxonomy"/>
+     </test> 
+     
+     <!--Test case with invalid lines -->
+     <test>
+          <param name="input1" value="lca_input3.taxonomy" ftype="taxonomy"/>
+          <param name="rank_bound" value="10" />
+          <output name="out_file1" file="lca_output3.taxonomy" ftype="taxonomy"/>
+     </test> 
  </tests>
<help>

    

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

[galaxy-dev] [hg] galaxy 3425: Bug fixes to LCA tool