[Bioperl-l] Re: How to convert ABI trace file to Phred file?

[Hong Xu]

Hi Aaron,

It works! Thank you so much for your prompt response and help.

I think the problem with abi.pm called from SeqIO.pm is that
SeqIO.next_seq()
returns a seq object although abi.next_seq() specifies to return a
Bio::SeqWithQuality object. Their return object types don't match!

Another problem is that SeqIO keeps writing the same sequnce again and
again. It could convert 175kb ABI trace file into 35M phred file (NOT
finish......)! And the actual phred file should be only 6kb!

I used the cvs version of bioperl-live and bioperl-ext. I will try to
install the
bioperl 1.2 stable release.

Thanks again for your help!

best regards,
Hong Xu      +1 919 684 3962
hong.xu@duke.edu  wwwchg.duhs.duke.edu


----- Original Message -----
From: "Aaron J Mackey" <ajm6q@virginia.edu>
To: "Hong Xu" <hxu@chg.duhs.duke.edu>
Cc: <bioinformatics@dieselwurks.com>; "Frank Zhao"
<fzhao@chg.duhs.duke.edu>; "Bioperl" <bioperl-l@bioperl.org>
Sent: Monday, January 06, 2003 2:41 PM
Subject: Re: How to convert ABI trace file to Phred file?


>
> Does adding this help?
>
> use Bio::Seq::SeqFactory;
> $ABIin->sequence_factory(
>   new Bio::Seq::SeqFactory(-verbose => $ABIin->verbose,
>                            -type => 'Bio::Seq::SeqWithQuality'
>   )
> );
>
> (After the $ABIin = new Bio::SeqIO ... bit)
>
> I'm not sure why abi.pm in the bioperl distribution doesn't set it's
> sequence factory to SeqWithQuality ... but perhaps the Staden read package
> didn't support reading abi trace quality??  If the above doesn't help you,
> then I'll dig deeper.
>
> -Aaron
>
> On Mon, 6 Jan 2003, Hong Xu wrote:
>
> > Hi Chad, Aaron,
> >
> > I have installed bioperl-ext & bioperl-live with Staden io_lib.
> > I want to convert ABI trace file to Phred file. I used SeqIO
> > module to do it. Here is the code:
> >
> > #!/usr/local/bin/perl -w
> > use strict;
> > use Bio::SeqIO;
> > use Getopt::Std;
> >
> > my %args;
> > getopt("ap", \%args);
> > if (!$args{a}) {
> >   die "Please specify the input ABI file name!";
> > }
> > if (!$args{p}) {
> >   die "Please specify the output PHD file name!";
> > }
> >
> > my $ABIin = new Bio::SeqIO( -format => "ABI", -file => "$args{a}" );
> > my $PHDout = new Bio::SeqIO( -format => "phd", -file => ">$args{p}" );
> >
> > while (my $seq = $ABIin->next_seq) {
> >     $PHDout->write_seq($seq);
> > }
> >
> > When I executed above code. The program asked for SeqWithQuality object.
> > I don't know how to define that object? I couldn't find related
document.
> > Could
> > you help me fix the problem?
> >
> > thanks,
> > Hong Xu      +1 919 684 3962
> > hong.xu@duke.edu  wwwchg.duhs.duke.edu
> >
> >
>
> --
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey@virginia.edu
>
>
>