[Bioperl-l] update to Bio::Tools::Run::EMBOSSacd

Brian Osborne brian_osborne at cognia.com
Mon Nov 1 15:14:56 EST 2004


This is done.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of smontgom at bcgsc.ca
Sent: Monday, October 25, 2004 11:33 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] update to Bio::Tools::Run::EMBOSSacd

Yo -

Can I pass on this code snippet for a CVS commit?

The newer version of EMBOSS removes the acdc parameter -acdtable.

So the Bio::Tools::Run::EMBOSSacd module needs this snippet added at line
158 (after the reset of the hash %OPT)

    my $version = `embossversion`;
    my $file;
    if ($version lt "2.8.0") {
        # reading from EMBOSS program acdc stdout (previous to version
       $file = `acdc $prog -help -verbose -acdtable 2>&1`;
    else {
        # reading from EMBOSS program acdtable stdout (equal to after 2.8.0)
        $file = `acdtable $prog -help -verbose 2>&1`;

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