[Bioperl-guts-l] [BioPerl - Bug #3190] RemoteBlast GAPCOSTS regular expression input

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Wed Mar 30 19:47:00 EDT 2011


Issue #3190 has been updated by Ali Walsh.


attempt to upload the patch

I am getting errors so I copied the code here, I realise that you are not supposed to but it is not very much code.

diff --git a/Bio/Tools/Run/RemoteBlast.pm b/Bio/Tools/Run/RemoteBlast.pm
index 31a655a..c8b3ca3 100644
--- a/Bio/Tools/Run/RemoteBlast.pm
+++ b/Bio/Tools/Run/RemoteBlast.pm
@@ -188,7 +188,7 @@ our %PUTPARAMS = (
     'ENTREZ_QUERY'      => '.*',
     'EXPECT'    => '\d+(\.\d+)?([eE]-\d+)?',    # Positive double
     'FILTER'    => '[LRm]',                     # L or R or m
-    'GAPCOSTS'  => '-?\d+(\.\d+)\s+i-?\d+(\.\d+)',
+    'GAPCOSTS'  => '-?\d+(\.\d+)\s+-?\d+(\.\d+)',
                                     # Two space separated float values
     'GENETIC_CODE'      => '([1-9]|1[1-6]|2(1|2))',     # 1..16,21,22
     'HITLIST_SIZE'      => '\d+',                       # Positive integer
----------------------------------------
Bug #3190: RemoteBlast GAPCOSTS regular expression input
https://redmine.open-bio.org/issues/3190

Author: Ali Walsh
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: 
Target version: 
URL: 


In the code for BEGIN in RemoteBlast,
the regular expression for the required form of input for the GAPCOSTS has an i in it that should not be there. The documents say two floats separated by a space and the i makes input of this type invalid.


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