qualifiers for for water/needle@ Bio::Factory::EMBOSS

[rafalcode]

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]

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

[bosborne]

Like this, yes?

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

[rafalcode]

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

[bosborne]

Done.

[rafalcode]

cheers, thanks.