[Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Nov 20 05:07:10 EST 2009


Hello

I was just wondering if anyone had had time to look into this?

I posted a bug: http://bugzilla.open-bio.org/show_bug.cgi?id=2937

Thanks
Mick

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of michael watson (IAH-C)
Sent: 27 October 2009 09:01
To: 'Jason Stajich'
Cc: bioperl-l
Subject: Re: [Bioperl-l] strand in Bio::SearchIO when parsing fasta35 output

Hi Jason

They both print 0 also.

A bug report it is

Mick

-----Original Message-----
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)
Cc: bioperl-l
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  
prints?

A full example report as a bug request will be next step if that  
doesn't resolve.

-jason
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   
> 0.0011
> 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
>
> Thanks
> Mick
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org


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