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

[陳彥璋]

Hi,

I'm processing chromate files (.abi 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