[Bioperl-l] phd format conversion.

[Brian Osborne]

Sankari,

If fasta is the only format available to you then you'll probably have to
create a SeqWithQuality object using the sequence in the fasta files. Take a
look at this link:

http://bioperl.org/Core/Latest/bptutorial.html#iii.7.6_incorporating_quality
_data_in_sequence_annotation_(seqwithquality)

Since there's no quality data in the fasta file you'll just have to make up
reasonable values.

If you're new to bioperl then I'd also recommend that you take a look at the
other bptutorial sections on the Seq object and on SeqIO as it's sounding
like you're going to be reading from and writing to sequence files.


Brian O.

-----Original Message-----
From: sankari thirumal [mailto:sankari_thirumal at yahoo.com]
Sent: Friday, September 12, 2003 12:15 PM
To: Brian Osborne
Subject: RE: [Bioperl-l] phd format conversion.

Dear sir,

I want use the phd format for SNP detection. Only phd format is accepted by
the software for SNP detection. SO it is mandatory for me to convert the
sequence to .phd format. Please help me in this regard.

with regards

sankari


Brian Osborne <brian_osborne at cognia.com> wrote:
Sankari,

I can't answer your question but I do have a couple of thoughts. First, you
might consider upgrading to version 1.2.2 or get the upcoming 1.2.3, there
are a number of important bug fixes in these 2 versions, version 1.0.1 is
quite old. Second, I'm wondering why you want to convert from fasta to phd,
since *phd files contain not just sequence but also quality scores for each
base. Fasta files, of course, don't have quality information. It sounds like
you're testing out various format conversions but this is one that normally
one would not choose to do. In fact in 1.2.2 this conversion isn't possible,
you get this error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: You must pass a Bio::Seq::SeqWithQuality object to write_scf as a
parameter named "SeqWithQuality"

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of sankari thirumal
Sent: Wednesday, September 10, 2003 12:27 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] phd format conversion.

Dear sir,

i'm using bioperl version 1.0.1. I could convert fasta to most of the
formats except phd. I'm sending the error mesaage. please explain me what i
should do.
the error message is as follows:

[root at Host0 bioperl-0.9.0]# perl conphd.pl
Bio/SeqIO/phd.pm: phd cannot be found
Exception Can't locate Bio/SeqIO/phd.pm in @INC (@INC contains:
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO.pm line 477.

For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
Can't use an undefined value as a symbol reference at conphd.pl line 9,
line 1.

i'll be grateful if could give suugestions to solve this problem

with regards
sankari






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