[Bioperl-l] searchIO bug?

Anders Stegmann anst at kvl.dk
Thu Feb 16 04:24:51 EST 2006


Hi! 
 
 
I am blasting a protein seq against an identical protein. 
I am trying to parse the protein header by using the query_description
method in the SearchIO module. 
After using the query_description method I use split / /      in order
to easily access the different header components. 
Here I discover that the query_description method is somehow introducing
a space between number 5 comma and the following chromosome position
number 
in the exon chromosome position list!? 
This truncates the list of exon chromosome positions from 7 to 4, later
yielding a wrong number of the introns counted. 
 
Is this a bug? 
 
Attached is: 
 
testblast1.pl: the blastprogram to run. 
 
Q0045 the seq that is used as both query and database seq. 
(Q0045 has to be formated in order to be used as a database: formatdb -i
Q0045 -p T -o F) 
 
 
Regards Anders. 

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