[Bioperl-l] phd format conversion.

[Brian Osborne]

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,
<GEN0> line 1.

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

with regards
sankari






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