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

[Aaron J Mackey]

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