[Bioperl-l] Trouble in converting abi files to phd files by Bio::SeqIO

[Aaron Mackey]

Doesn't Bio::SeqIO::abi fall back to Chad's pure-perl solution if the
bioperl-ext modules are not installed?

Regardless, can you get a dump of the $seq objects before you hand them off
to Bio::SeqIO::phd -- have the qual scores already been lost (problem with
the abi reader), or not (problem with the phd writer)?

And a basic question -- I assume your .abi files actually have quality
values in them (not all do)?

-Aaron


On Wed, Jul 21, 2010 at 8:09 PM, Chris Fields <cjfields at illinois.edu> wrote:

> It's very possible this is due to API changes within io_lib, but I can't be
> sure.  Aaron, any idea?
>
> Just to note, we no longer recommend using the bioperl-ext modules, mainly
> b/c they have not been actively maintained, so much so that updating them to
> use the current API is quite difficult (might involve some extensive
> refactoring).  The BioLib project, however, has perl bindings to io_lib.  If
> one had time they could incorporate the BioLib io_lib bindings into bioperl,
> but I believe ABI support was removed a while ago so that will be
> problematic.
>
> chris
>
> On Jul 19, 2010, at 2:11 AM, 陳彥璋 wrote:
>
> > Hi,
> >
> > I'm processing chromate files (.ab1 format) with BioPerl-1.6.1,
> > bioperl-ext-1.5.1, and io-lib-1.8.11;
> > my OS was 32-bit, Centos 5.2.
> > When I convert abi-format files to phd-format files,
> > the value of quality of all bases are '0', and the value of
> > trace_index of all bases are undefined.
> > Is there any possible reason leading to this problem?
> >
> > Besides, it claims that CALL_METHOD is phred and PHRED_VERSION is
> > 0.980904.e in phd files;
> > if this is the case, where can I find phred executers?
> >
> > The following is the code utilizing BioPerl and results from BioPerl
> > and Phred respectively:
> > ==============================================
> > #!/usr/bin/perl -w
> > unshift(@INC, "/opt/BioPerl-1.6.1/");
> > unshift(@INC, "/opt/bioperl-ext");
> > use strict;
> > use Bio::SeqIO;
> >
> > my $inputfilename='./HMA040184H12.T3.ab1';
> > my $outputfilename='test11.phd';
> >
> > my  $in  = Bio::SeqIO->new(-file => "$inputfilename",
> >                       -format => 'abi');
> >
> > my  $out = Bio::SeqIO->new(-file => ">$outputfilename",
> >                       -format => 'phd');
> >
> > while ( my $seq = $in->next_seq() ) {
> >      for my $curr(1 ..  $seq->length()) {
> >              print "[",$seq->qualat($curr),"]:";
> >              print "[",$seq->trace_index_at($curr),"]\t";
> >      }
> >      $out->write_seq($seq);
> >      last;
> > }
> >
> > ================== test11.phd (by Bio::SeqIO) =================
> > BEGIN_SEQUENCE (null)
> >
> > BEGIN_COMMENT
> >
> > CHROMAT_FILE: unknown
> > ABI_THUMBPRINT: 0
> > PHRED_VERSION: 0.980904.e
> > CALL_METHOD: phred
> > QUALITY_LEVELS: 99
> > TIME: Mon Jul 19 11:59:09 2010
> > TRACE_ARRAY_MIN_INDEX: 0
> > TRACE_ARRAY_MAX_INDEX: unknown
> > CHEM: unknown
> > DYE: unknown
> >
> > END_COMMENT
> >
> > BEGIN_DNA
> > A 0
> > G 0
> > G 0
> > G 0
> > G 0
> > .
> > .
> > .
> > .
> >
> > G 0
> > T 0
> > T 0
> > G 0
> > T 0
> > C 0
> > G 0
> > C 0
> > T 0
> > A 0
> > C 0
> > END_DNA
> >
> > END_SEQUENCE
> >
> > ================== .phd (by phred 0.020425.c) =======================
> > BEGIN_SEQUENCE HMA040184H12.T3.ab1
> >
> > BEGIN_COMMENT
> >
> > CHROMAT_FILE: HMA040184H12.T3.ab1
> > ABI_THUMBPRINT: 0
> > PHRED_VERSION: 0.020425.c
> > CALL_METHOD: phred
> > QUALITY_LEVELS: 99
> > TIME: Fri Jul  9 16:20:59 2010
> > TRACE_ARRAY_MIN_INDEX: 0
> > TRACE_ARRAY_MAX_INDEX: 11905
> > TRIM: 38 900 0.0500
> > TRACE_PEAK_AREA_RATIO: 0.0630
> > CHEM: term
> > DYE: big
> >
> > END_COMMENT
> >
> > BEGIN_DNA
> > a 11 2
> > g 11 13
> > g 11 22
> > a 11 37
> > a 11 52
> > g 8 65
> > c 6 76
> > t 6 91
> > c 6 97
> > .
> > .
> > .
> > a 14 11840
> > c 16 11849
> > a 16 11861
> > a 12 11873
> > c 12 11885
> > g 12 11897
> > END_DNA
> >
> > END_SEQUENCE
> > ================================================
> > Sincerely yours,
> > Yen-Chang Chen
> >
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>