[Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output
michael watson (IAH-C)
michael.watson at bbsrc.ac.uk
Tue Oct 27 05:01:12 EDT 2009
They both print 0 also.
A bug report it is
From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason Stajich
Sent: 26 October 2009 18:46
To: michael watson (IAH-C)
Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output
Is this -m9 -d 0 output or standard default? I think the strand is
parsed in the HSP parsing.
Can you double check what $hsp->query->strand and $hsp->hit->strand
A full example report as a bug request will be next step if that
On Oct 26, 2009, at 10:04 AM, michael watson (IAH-C) wrote:
> Dear all
> Where does this go? Perhaps I am doing something wrong.
> Fasta35 output puts the strand in the hit list at the top:
> cluster_99033:3 ( 23) [r] 115 37.9
> cluster_79238:1 ( 27) [f] 126 38.0 0.00097 0.963
> 0.963 27
> The [r] stands for reverse and the [f] stands for forward.
> There is also the text "rev-comp" after the hit line further down.
> However, when I parse fasta35 output using SearchIO and output the
> strand of the HSP:
> print $hsp->strand('hit'), ",";
> print $hsp->strand('query'), "\n";
> This simply prints out 0, 0 (I assume 0 is the default in BioPerl
> for "I don't know which strand it's on").
> So the information is there, but it's not getting parsed.
> Alternatively, I've missed something and will feel a bit foolish.
> Currently using BioPerl 1.6.0
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jason.stajich at gmail.com
jason at bioperl.org
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