[Bioperl-l] [Bioperl-guts-l] Notification: incoming/920 (fwd)

[Jason Stajich]

Brian -
 
Thanks for the bug submission, no one has worked on this module in a long
time.  We didn't even have any testfiles so there are no tests designed
for this module which explains why you are having problems.  Would you be
willing to submit a test scf file to help us write some good tests for it
and I suspect we can track down the correct way to fix this bug.  I
suspect it is rooted in our new methods for handling filehandles all in
one place and this module did not get updated.  

Thanks.

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/ 


---------- Forwarded message ----------
Date: Thu, 8 Mar 2001 14:13:54 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/920

JitterBug notification

new message incoming/920

Message summary for PR#920
	From: bdesany@houston.rr.com
	Subject: next_seq hangs it scf
	Date: Thu, 8 Mar 2001 14:13:53 -0500
	0 replies 	0 followups

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>From bdesany@houston.rr.com Thu Mar  8 14:13:53 2001
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Date: Thu, 8 Mar 2001 14:13:53 -0500
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From: bdesany@houston.rr.com
To: bioperl-bugs@bioperl.org
Subject: next_seq hangs it scf

Full_Name: Brian Desany
Module: Bio::SeqIO::scf
Version: 0.7
PerlVer: 5.005_03
OS: sparc-sun-solaris2
Submission from: reserved7.bioch.bcm.tmc.edu (128.249.56.248)


Hi,

In the next_seq method of Bio::SeqIO::scf, line 136 has:

unless 12 == read(STDIN, $buffer, 12);

The result is that when you try to get information from an SCF file, it sits
there waiting on STDIN.

Changing STDIN to $fh fixes this (or so it seems to me :).

Of course, there's always the possibility I'm using this wrong, but taking the
example from SeqIO.pm:

use Bio::SeqIO;

    $in  = Bio::SeqIO->newFh(-file => "inputfilename" , '-format' => 'Fasta');
    $out = Bio::SeqIO->newFh('-format' => 'EMBL');

    # World's shortest Fasta<->EMBL format converter:
    print $output $_ while <$in>;

Switching out Fasta for scf elicits this behavior.

-Brian.


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