Fisrt pass on taxonomic rank fetcher

2026-09-24 16:30:27 +08:00 · 2008-03-03 19:40:36 +00:00
parent 135c9a0377
commit 9dca050a79
3 changed files with 143 additions and 0 deletions
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+33001686	9443	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Primates	n	n	n	n	n	n	n	n	n	n
+23236241	9604	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Primates	Haplorrhini	Hominoidea	Hominidae	n	n	n	n	n	n	n
+12583	9606	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Primates	Haplorrhini	Hominoidea	Hominidae	n	n	n	Homo	n	Homo sapiens	n
+410771	40674	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	n	n	n	n	n	n	n	n	n	n	n	n
+2286205	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
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+<tool id="Fetch Taxonomic Ranks" name="Fetch Taxonomic Ranks" version="1.0.0">
+  <description>from a list of GIs</description>
+  <command interpreter="python">tax.py $input $out_file1 -c $giField</command>
+  <inputs>
+    <param format="tabular" name="input" type="data" label="Fetch sequences corresponding to Query"></param>
+    <param name="giField" label="GIs column" type="data_column" data_ref="input" />
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="taxonomyGI.txt"/>
+      <param name="giField" value="1"/>
+      <output name="out_file1" file="taxonomyGI.dat"/>
+    </test>
+  </tests>
+
+  <help>
+
+.. class:: infomark
+
+Use *Filter and Sort->Filter* to restrict output of this tool to desired taxonomic ranks. You can also use *Text Manipulation->Cut* to remove unwanted columns from the output.
+
+------
+
+**What it does**
+
+Fetches taxonomic information for a list of GI numbers (sequiences identifiers used by teh National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov).
+
+-------
+
+**Example**
+
+Suppose you have BLAST output that looks like this::
+  
+   +-----------------------+----------+----------+-----------------+------------+------+--------+
+   | queryId               | targetGI | identity | alignmentLength | mismatches | gaps | score  |
+   +-----------------------+----------+----------+-----------------+------------+------+--------+
+   | 1L_EYKX4VC01BXWX1_265 |  1430919 |    90.09 |             212 |         15 |    6 | 252.00 | 
+   | 1L_EYKX4VC01BXWX1_265 |   516142 |    90.09 |             212 |         15 |    6 | 252.00 | 
+   +-----------------------+----------+----------+-----------------+------------+------+--------+
+
+and you want to obtain full taxonomic representation for GIs listed in *targetGI* column.  The output of this tool will add 21 columns to the input data shown above. The 21 columns will correspond to::
+
+        'root'        :1,
+        'superkingdom':2,
+        'kingdom'     :3,
+        'subkingdom'  :4,
+        'superphylum' :5,
+        'phylum'      :6,
+        'subphylum'   :7,
+        'superclass'  :8,
+        'class'       :9,
+        'subclass'    :10,
+        'superorder'  :11,
+        'order'       :12,
+        'suborder'    :13,
+        'superfamily' :14,
+        'family'      :15,
+        'subfamily'   :16,
+        'tribe'       :17,
+        'subtribe'    :18,
+        'genus'       :19,
+        'subgenus'    :20,
+        'species'     :21,
+        'subspecies'  :22
+
+
+
+
+
+</help>
+</tool>
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+#!/usr/bin/env python
+
+"""
+Identify full taxonomic standing for sequences identified by gi number
+
+usage: %prog gi_list_file out_file
+    -c, --cols=N: Number of column containing gi within the gi_list file
+
+    gi_list_file - user's input containing gi's in the column specified by option -c
+
+    taxonomy_db - database containing collapsed NCBI taxonomy generated by prepareTaxonomy.sh script 
+    distributed with Galaxy. See prepareTaxonomy.readme for information on how to generate
+    necessary files
+    
+"""
+
+import pkg_resources
+pkg_resources.require( 'bx-python' )
+pkg_resources.require( 'pysqlite' )
+import traceback
+import fileinput
+from pysqlite2 import dbapi2 as sqlite
+from warnings import warn
+from bx.cookbook import doc_optparse
+import string, sys
+
+TAXONOMY = '/Users/anton/galaxy/static/taxonomy/taxonomy.db'
+
+def main():
+    
+    options, args = doc_optparse.parse( __doc__ )
+    
+    if len(args) < 2:
+        sys.stderr.write('Not enough arguments\n')
+        sys.exit(0)    
+        
+    try:
+        gi_fname, out_fname = args
+        giCol = int( options.cols ) - 1
+    except:
+        doc_optparse.exception
+        
+    con = sqlite.connect(TAXONOMY)
+    cur = con.cursor() 
+    fg = open(gi_fname, 'r')
+    of = open( out_fname, "w" )
+    
+    try:
+        for line in fg:
+                field = string.split(line.rstrip(), '\t')
+                sqlTemplate = string.Template('select gi2tax.gi, tax.* from gi2tax left join tax on gi2tax.taxId = tax.taxId where gi2tax.gi = $gi') 
+                sql = sqlTemplate.substitute(gi = int(field[giCol]))
+                cur.execute(sql)
+
+                for item in cur.fetchall():
+                    ranks = string.split(item[2], ",")
+                    print >> of, str(item[0]) + "\t" + str(item[1]) + "\t" + "\t".join(ranks) 
+
+    finally:
+        fg.close()
+        of.close()
+        
+if __name__ == "__main__":
+    main()