[Bioperl-l] phd format conversion.

[James D. White]

Sankari,

Phd files are the normal output of the Phred basecalling program written 
by Phil Green.
If you have the original data files from a sequencer (for example,  ab1 
or scf files), you
could run Phred to produce phd files with  real quality values. This is 
not a Bioperl
solution, but may be a better one if you have the original trace file 
data, not just the
sequence. If all you have is the sequence, then other solutions are 
required.

For this specific problem I do have a program, fastaq2phd, to create phd 
files from
a fasta file. The program may be found at: 
<http://www.genome.ou.edu/informatics.html>.
This is not a Bioperl program. It was written before I knew about 
Bioperl. If this is
all the function you need it should work, but a Bioperl solution would 
probably be a
better choice if you need to integrate it with other code.

James D. White   (jdw at ou.edu)
Department of Chemistry and Biochemistry
University of Oklahoma
620 Parrington Oval, Room 313
Norman, OK 73019-3051

>Date: Fri, 12 Sep 2003 12:33:18 -0400
>From: "Brian Osborne" <brian_osborne at cognia.com>
>Subject: RE: [Bioperl-l] phd format conversion.
>To: "sankari thirumal" <sankari_thirumal at yahoo.com>
>Cc: bioperl-l at bioperl.org
>Message-ID: <GAEDKMGOKFBLJPKCLKCCKEOMDBAA.brian_osborne at cognia.com>
>Content-Type: text/plain; charset="us-ascii"
>
>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
>
>  
>