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

[Hong Xu]

I think one ABI trace file should have only one sequence. And
I checked the output phred file. Those sequences were exactly
the same. Yes, I will remove the while loop.

Thank you so much 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: "Frank Zhao" <fzhao@chg.duhs.duke.edu>; "Bioperl"
<bioperl-l@bioperl.org>
Sent: Monday, January 06, 2003 4:36 PM
Subject: Re: How to convert ABI trace file to Phred file?


>
> For now I'd suggest removing the while() loop.
>
> Can ABI files have more than one sequence in them?
>
> -Aaron
>
> On Mon, 6 Jan 2003, Hong Xu wrote:
>
> > 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
> > >
> > >
> > >
> >
>
> --
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey@virginia.edu
>
>
>