Filter BLAST by taxid

[peterjc]

See email and proposed solution from Thomas Berner on the galaxy-dev list http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-June/015103.html

He suggested adding a new taxid_name.loc file, e.g.

$ more taxid_name.loc 
Hordeum vulgare 4513
Oryza sativa    4530
Sorghum bicolor 4558
Triticum aestivum       4565
Triticum urartu 4572
Brachypodium distachyon 15368

And new parameter,

+        <conditional name="taxon">
+            <param name="taxid_selector" type="select" label="Filter by taxon id (taxid)?">
+              <option value="no" selected="True">No filtering</option>
+              <option value="yes">Filter by user-selected taxid</option>
+            </param>
+           <when value="yes">
+                <repeat name="multitax" title="taxid" min="1">
+                       <param name="taxid" label="taxid" type="select">
+                               <options from_file="taxid_name.loc">
+                                       <column name="name" index="0"/>
+                                       <column name="value" index="1"/>
+                               </options>
+                       </param>
+                       <param name="exclude" label="exlude" type="boolean"/> 
+                 </repeat>
+           </when>
+       </conditional>

with associated Cheetah syntax for the command string:

+#if $taxon.taxid_selector == "yes":
+       #for $r in $taxon.multitax:
+               #if $r.exclude:
+                       -negative_gilist $r.taxid
+               #else
+                       -window_masker_taxid "$r.taxid"
+               #end if
+       #end for
+#end if

The -window_masker_taxid option seems to make sense (although may require some setup work - see http://www.ncbi.nlm.nih.gov/books/NBK1763/ for details),

 -window_masker_taxid 
   Enable WindowMasker filtering using a Taxonomic ID

However, for exclusion is it possible to give a taxid to -negative_gilist (or -gilist)?

[peterjc]

Note that only blastn provides -window_masker_taxid (not available in blastp, blastx, tblastn, tblastx).

[peterjc]

See also my BLAST+ Christmas Wish List http://blastedbio.blogspot.com/2014/12/blast-christmas-wish-list.html entry Taxonomy filters