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bioperl / bioperl-run

BioPerl wrappers
http://bioperl.org
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qualifiers for for water/needle@ Bio::Factory::EMBOSS #50

Closed rafalcode closed 7 years ago

rafalcode commented 7 years ago

The latest docs for this module refer to "-asequence" and "-seqall" for these two tools, the latter seems to be rejected. I'm on Debian Testing (Stretch) which has EMBOSS 6.6.0. I found using EMBOSS actual docs that "-sequencea" and "-sequenceb" work instead.

rafalcode commented 7 years ago

Sorry error: non-working is "-sequencea" and "-seqall". Working is "-asequence and "-bsequence"

bosborne commented 7 years ago

Like this, yes?

    $water->run(
        {   -asequence => $seq,
            -bsequence => \@amino,
            -gapopen   => '10.0',
            -gapextend => '0.5',
            -outfile   => $wateroutfile
        }
    );
rafalcode commented 7 years ago

yes, exactly. that's the one that works. perl hash keys matching the EMBOSS options exactly.

bosborne commented 7 years ago

Done.

rafalcode commented 7 years ago

cheers, thanks.