[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1267 (fwd)

[Jason Stajich]

Rich - what version of bioperl are you using, I think I may have already
fixed this bug but I'll have to go back and check.



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

---------- Forwarded message ----------
Date: Wed, 9 Oct 2002 19:59:21 -0400
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1267

JitterBug notification

new message incoming/1267

Message summary for PR#1267
	From: Rich LeDuc <rleduc@uiuc.edu>
	Subject: Possible bug in SeqIO
	Date: Wed, 09 Oct 2002 19:38:36 -0500
	0 replies 	0 followups

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Date: Wed, 09 Oct 2002 19:38:36 -0500
To: bioperl-bugs@bioperl.org
From: Rich LeDuc <rleduc@uiuc.edu>
Subject: Possible bug in SeqIO
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Sorry for not using the automated system - but as I am not associated with
bioperl development I wasn't sure if I should...

Anyway, I am using SeqIO to write quality files something like this:

$qual_out = Bio::SeqIO->new(-file => "$my_file", '-format' => 'qual');
$qual_out->write_seq(-source => $seq);

Where $seq is a sequence defined earlier in the script.  When I do this,
the files come out looking fine, except there is a single blank space at
the end of each line.  This space was not in the original file that $seq
was read from...

These extra spaces cause Cap3, as we are running it, to fail.

Please let me know if there is additional information I can provide.

Thanks,

Rich

-------------------------------------------------------
Richard LeDuc
Research Programmer
Bioinformatics Unit
W.M. Keck Center for Comparative and Functional Genomics
Biotechnology Center
University of Illinois at Urbana-Champaign



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