[Bioperl-guts-l] [15738] bioperl-live/trunk/t/data/frac_problems2.blast: added spaces to end of homology strings:

Mark Allen Jensen maj at dev.open-bio.org
Tue Jun 2 11:32:00 EDT 2009


Revision: 15738
Author:   maj
Date:     2009-06-02 11:32:00 -0400 (Tue, 02 Jun 2009)

Log Message:
-----------
added spaces to end of homology strings:

here's a weird parsing 'bug': In a blastn, one will have an hsp

100 atcg 103
    || |
400 atgg 397

No problem, the query string is 'atcg'
            the match string is '|| |'
            the hit   string is 'atgg'

But if we have

100 atcg 103
    |||
400 atcc 397

then        the query string is 'atcg'
	    the match string is '|||'
	    the hit   string is 'atcc'

That is, the match string is missing the space at the end. This 
may be a bug in the report generating program. 

Modified Paths:
--------------
    bioperl-live/trunk/t/data/frac_problems2.blast

Modified: bioperl-live/trunk/t/data/frac_problems2.blast
===================================================================
--- bioperl-live/trunk/t/data/frac_problems2.blast	2009-06-02 15:18:33 UTC (rev 15737)
+++ bioperl-live/trunk/t/data/frac_problems2.blast	2009-06-02 15:32:00 UTC (rev 15738)
@@ -89,7 +89,7 @@
 
 
 Query: 192    gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccacctcagctgaagcggcta 251
-              ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
+              ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| 
 Sbjct: 768635 gtctgcgctcgccgtcgtcgcacgctctgtgctcctgcaccccctcagctgaagcggctg 768694
 
 
@@ -125,7 +125,7 @@
 
 
 Query: 959    ttttccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttt 1018
-              |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
 Sbjct: 769467 ttttccgccacggccggtaacaactatgtaacctttcactatggaaaactgcaaaagttc 769526
 
 




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