# HG changeset patch # User devteam # Date 1390498268 18000 # Node ID e7d70880851e4e1ac3a19c75e5fe3bd4e5428907 Imported from capsule None diff -r 000000000000 -r e7d70880851e t2t_report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/t2t_report.xml Thu Jan 23 12:31:08 2014 -0500 @@ -0,0 +1,72 @@ + + + + taxonomy + + taxonomy2tree $input 0 /dev/null $out_file1 0 + + + + + + + + taxonomy2tree + + + + + + + + + + + +**What it does** + +Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks. + +------ + +**Example** + +Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation:: + + 9916 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n + 9606 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n + +Running this tool will generate the following output:: + + Rank Rank Name Count + ------------------------------------- + root root 2 + superkingdom Eukaryota 2 + kingdom Metazoa 2 + phylum Chordata 2 + subphylum Craniata 2 + superclass Gnathostomata 2 + class Mammalia 2 + superorder Euarchontoglires 1 + superorder Laurasiatheria 1 + order Primates 1 + suborder Haplorrhini 1 + suborder Ruminantia 1 + superfamily Hominoidea 1 + family Bovidae 1 + family Hominidae 1 + subfamily Bovinae 1 + genus Bos 1 + genus Homo 1 + species Bos taurus 1 + species Homo sapiens 1 + +The output is sorted on Rank and then on Rank Name. + +.. class:: warningmark + +**Note** that this tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not. + + + + diff -r 000000000000 -r e7d70880851e test-data/t2t_report.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t2t_report.tabular Thu Jan 23 12:31:08 2014 -0500 @@ -0,0 +1,15 @@ +root root 5 +superkingdom Eukaryota 5 +kingdom Metazoa 5 +phylum Chordata 5 +subphylum Craniata 5 +superclass Gnathostomata 5 +class Mammalia 5 +superorder Euarchontoglires 4 +order Primates 4 +suborder Haplorrhini 3 +superfamily Hominoidea 3 +family Hominidae 3 +genus Homo 2 +species Homo sapiens 2 +subspecies Homo sapiens neanderthalensis 1 diff -r 000000000000 -r e7d70880851e test-data/taxonomyGI.taxonomy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/taxonomyGI.taxonomy Thu Jan 23 12:31:08 2014 -0500 @@ -0,0 +1,5 @@ +9606 9606 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n 12583 +40674 40674 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n n n n n n n n n n n n n 410771 +63221 63221 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens Homo sapiens neanderthalensis 2286205 +9604 9604 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n n n n n 23236241 +9443 9443 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates n n n n n n n n n n 33001686 \ No newline at end of file diff -r 000000000000 -r e7d70880851e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jan 23 12:31:08 2014 -0500 @@ -0,0 +1,6 @@ + + + + + +