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

[Chris Fields]

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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