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

[Aaron Mackey]

Hmm, perhaps I'm thinking about the SCF code, not the ABI code.

-Aaron

On Wed, Jul 21, 2010 at 10:41 PM, Chris Fields <cjfields at illinois.edu>wrote:

> Nope; doesn't appear to be a pure-perl parser for this.  Was there one?
>
> chris
>
> On Jul 21, 2010, at 7:36 PM, Aaron Mackey wrote:
>
> > 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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> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >
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