[Bioperl-l] needle parser in bioperl?

neeti somaiya neetisomaiya at gmail.com
Fri Dec 15 00:21:42 EST 2006


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


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