[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1109 (fwd)

[Jason Stajich]

Do you only have 4 queries in the file?  You're only printing the query
name.  You're also calling next_result twice in the same loop - so you're
going to skip an entry each loop iteration.  Are you getting any warnings
or errors?  We have tested this on many multi-sequence reports - what
version of blast and which blast (t)blast(n|p|x) are you using?

#This code will only print the queries name and length for each of the
#results.

use Bio::SearchIO;

my($filename) = "blast.cnone.cnone.txt";

my($searchio) = new Bio::SearchIO(-format => 'blast', -file => $filename);

while ($result = $searchio->next_result)
{
  print "  Query \"", $result->query_name, "\" (", $result->query_length,
"
pb)\n";

# DELETE THIS LINE!  $result = $searchio->next_result();
}


-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Wed, 27 Feb 2002 03:03:42 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1109

JitterBug notification

new message incoming/1109

Message summary for PR#1109
	From: aurelien.mazurie@free.fr
	Subject: A big bug (i think) for the BLAST parser !
	Date: Wed, 27 Feb 2002 03:03:41 -0500
	0 replies 	0 followups

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>From aurelien.mazurie@free.fr Wed Feb 27 03:03:41 2002
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Date: Wed, 27 Feb 2002 03:03:41 -0500
Message-Id: <200202270803.g1R83fkO005874@pw600a.bioperl.org>
From: aurelien.mazurie@free.fr
To: bioperl-bugs@bioperl.org
Subject: A big bug (i think) for the BLAST parser !

Full_Name: Aurelien Mazurie
Module: Bio::SearchIO
Version: 1.0-alpha
PerlVer: v5.6.1 (ActivePerl)
OS: Win2000 pro / Linux
Submission from: (NULL) (134.157.194.52)


First, apologizes for my english =)

Maybe it's me, but when i try to use this piece of code:

use Bio::SearchIO;

my($filename) = "blast.cnone.cnone.txt";

my($searchio) = new Bio::SearchIO(-format => 'blast', -file => $filename);

while ($result = $searchio->next_result)
 {
  print "  Query \"", $result->query_name, "\" (", $result->query_length, "
pb)\n";

  $result = $searchio->next_result();
 }


The result is that the script print on screen only an entry on two of the
original BLAST report file. Strange, isn't it ? So, what is the problem ? The
result is the same over different BLAST files, and i DO use BioPerl to do the
job, since i have 700 entries in different files !

PLEASE, help me ! This job is urgent, so if we can found and fix this problem...
quickly, i will be happy =)

(note: the problem is the same under Linux)

 Aurelien Mazurie
 (from France =)


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