diff tools/blast_rbh/blast_rbh.xml @ 5:c84b6c21e3d4 draft

Uploaded v0.1.0e, test TBLASTX mode; more columns in output

--- a/tools/blast_rbh/blast_rbh.xml	Mon May 19 13:39:55 2014 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Tue May 20 06:33:08 2014 -0400
@@ -108,6 +108,15 @@
             <output name="output" file="rbh_none.tabular" ftype="tabular"/>
         </test>
         <test>
+            <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
+            <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
+            <param name="dbtype" value="nucl"/>
+            <param name="nucl_type" value="tblastx"/>
+            <param name="identity" value="0.0"/>
+            <param name="q_cover" value="0.0"/>
+            <output name="output" file="rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/>
+        </test>
+        <test>
             <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta"/>
             <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta"/>
             <param name="dbtype" value="nucl"/>
@@ -124,24 +133,31 @@
 for each, runs reciprocal BLAST searchs (*A vs B*, and *B vs A*), optionally
 filters the HSPs, and then compiles a list of the reciprocal best hits (RBH).
 
-The output from this tool is a tabular file containing eight columns, with
+The output from this tool is a tabular file containing multiple columns, with
 information about the BLAST matches used:
 
-====== =================================
+====== ==================================
 Column Description
------- ---------------------------------
+------ ----------------------------------
      1 ID from *species A*
      2 ID from *species B*
-     3 Bitscore
-     4 Percentage identity
-     5 Query coverage from *A vs B*
-     6 Query coverage from *B vs A*
-====== =================================
+     3 Length of sequence *A*
+     4 Length of sequence *B*
+     5 Percentage of sequence *A* covered
+     6 Percentage of sequence *B* covered
+     7 HSP alignment length
+     8 HSP percentage identity
+     9 HSP bitscore
+====== ==================================
 
-These values correspond to the ``bitscore``, ``pident`` and ``qcovhsp``
-values in the BLAST+ tabular output. For the bitscore and percentage identity
-the values for *A vs B* and *B vs A* are typically the same, so their minimum
-is shown. The coverage values differ according to the query lengths.
+These values correspond to the ``qseqid``/``sseqid``, ``qlen``/``slen``,
+``qcovhsp``, ``length``, ``pident`` and ``bitscore`` values in the BLAST+
+tabular output.
+
+For the alignment length, bitscore and percentage identity the values for
+*A vs B* and *B vs A* are typically the same, so their minimum is shown.
+The coverage values are given by the HSP alignment length divided by the
+sequence length (adjusted by a factor of three for TBLASTX).
 
 .. class:: warningmark