# HG changeset patch
# User devteam
# Date 1390832777 18000
# Node ID 592acb9505fc208f2e2505f38c3250262e1b258a
Imported from capsule None
diff -r 000000000000 -r 592acb9505fc t2t_report.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/t2t_report.xml Mon Jan 27 09:26:17 2014 -0500
@@ -0,0 +1,72 @@
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+ taxonomy
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+ taxonomy2tree $input 0 /dev/null $out_file1 0
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+ taxonomy2tree
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+**What it does**
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+Given taxonomy representation (produced by *Taxonomy manipulation->Fetch Taxonomic Ranks* tool) this utility computes a summary of all taxonomic ranks.
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+------
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+**Example**
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+Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation::
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+ 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
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+Running this tool will generate the following output::
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+ 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
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+The output is sorted on Rank and then on Rank Name.
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+.. class:: warningmark
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+**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.
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diff -r 000000000000 -r 592acb9505fc test-data/t2t_report.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/t2t_report.tabular Mon Jan 27 09:26:17 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 592acb9505fc test-data/taxonomyGI.taxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomyGI.taxonomy Mon Jan 27 09:26:17 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 592acb9505fc tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Jan 27 09:26:17 2014 -0500
@@ -0,0 +1,6 @@
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