[Bioperl-l] needle parser in bioperl?

neeti somaiya neetisomaiya at gmail.com
Fri Dec 15 07:46:08 EST 2006


I ran needle like this

/usr/local/bin/./needle SEQ_1.REF seq_of_contig1 -aformat fasta 1.out

Please find the output attached.

When I run the following :-

use Bio::SearchIO;

my $io = Bio::SearchIO->new(-file   => "1.out",
                           -format => "fasta" );

while ( my $result = $io->next_result() )
{
       while( my $hit = $result->next_hit)
      {

               print "yes\n";
       }
}


It says :-

-------------------- WARNING ---------------------
MSG: unrecognized FASTA Family report file!
---------------------------------------------------

What should I do?

~Neeti.

On 12/15/06, Fairley, Derek <Derek.Fairley at bll.n-i.nhs.uk> wrote:
>
> Neeti,
>
> In lieu of a response from a BioPerl guru... why not use Needle to
> generate your pairwise alignment in fasta format, rather than msf format?
> The sequence you want should correspond to a single HSP which you can get
> directly from the fasta alignment with Bio::SearchIO:
> http://www.bioperl.org/wiki/Module:Bio::SearchIO. You may not need to use
> Bio::AlignIO at all.
>
> Derek.
>
>
> -----Original Message-----
> From: neeti somaiya [mailto:neetisomaiya at gmail.com]
> Sent: 15 December 2006 05:22
> To: Fairley, Derek; bioperl-l
> Subject: Re: [Bioperl-l] needle parser in bioperl?
>
> Hi,
>
> Thanks a lot for your response.
> I ran needle like this
> /usr/local/bin/./needle SEQ_1.REF seq_of_contig1 -aformat msf 1.out
> It gave me the output in format msf.
> But now my problem is, if I use Bio::AlignIO module of Bioperl, how can I
> get the alignment start and stop coordinates on the sequence. I mean
> something like hsp->query->start which gives us the alignment start position
> on query sequence in a blast output when using Bio::SearchIO.
> Please help.
> Like I explained with an example in my previous mail, I want the
> coordinate where the alignment starts on the sequence.
>
> ~Neeti.
> On 12/14/06, Fairley, Derek <Derek.Fairley at bll.n-i.nhs.uk> wrote:
> Neeti,
>
> From http://emboss.sourceforge.net/apps/cvs/needle.html :
>
> "The results can be output in one of several styles by using the
> command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of
> the required format. Some of the alignment formats can cope with an
> unlimited number of sequences, while others are only for pairs of sequences.
>
> The available multiple alignment format names are: unknown, multiple,
> simple, fasta, msf, trace, srs
>
> The available pairwise alignment format names are: pair, markx0, markx1,
> markx2, markx3, markx10, srspair, score
>
> See: http://emboss.sf.net/docs/themes/AlignFormats.html for further
> information on alignment formats."
>
> Not sure based on this whether you can get pairwise alignment in .msf
> format; can't think of a good reason why not. The BioPerl Align::IO module
> will allow you to parse alignments in .msf format.
>
> HTH,
>
> Derek.
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:
> bioperl-l-bounces at lists.open-bio.org] On Behalf Of neeti somaiya
> Sent: 14 December 2006 08:03
> To: Chris Fields; bioperl-l
> Subject: Re: [Bioperl-l] needle parser in bioperl?
>
> How do I run needle specifying that I want the MSF format, on a linux box?
> The help doesnt show me any format option. Is there anything available to
> pasre MSF format?
> Please find an example alignment file attached. Here the seq_of_contig
> aligns with the reference sequence (i.e. SEQ_1.REF) starting at position
> (coordinate) 8918 of SEQ_1.REF. I basically want this coordinate from the
> output alignment, how can I parse the result to get this?
>
> On 12/12/06, Chris Fields <cjfields at uiuc.edu > wrote:
> >
> >
> > On Dec 12, 2006, at 6:14 AM, neeti somaiya wrote:
> >
> > > Hi,
> > >
> > > Does anyone know of a bioperl parser for needle output, basically I
> > > won't
> > > where the target sequence aligns on the template (i.e. coordinate
> > > on the
> > > template where the taget aligns).
> > >
> > > --
> > > -Neeti
> > > Even my blood says, B positive
> >
> > I answered this a number of months back:
> >
> > http://tinyurl.com/yzlbx5
> >
> > Basically, newer versions of EMBOSS have changed the output for the
> > AlignIO::emboss parser (which parses needle). I don't believe the
> > parser has been fixed to deal with that, but Jason has pointed out
> > you can use MSF output when running needle, then parse using AlignIO
> > with the format set to 'msf'.
> >
> > chris
> >
>
>
>
> --
> -Neeti
> Even my blood says, B positive
>
>
>
> --
> -Neeti
> Even my blood says, B positive
>



-- 
-Neeti
Even my blood says, B positive
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