[Bioperl-l]ABI.pm and .ab1 files

Kevin Roland Viel kviel at emory.edu
Wed Apr 28 18:56:27 EDT 2004


   Thanks.  I diverted some attention to perl, but just not enough :(

   This still frustrates me, but I have found a kludge.  I use phred so I
just added the -cd <directory> -cp 2.  The SCF file produced has a 128
byte header followed by the data of interest.  I read this file directly
using SAS (using the S370FPIB2. informat).  The file is in big endian
format.  If anyone following this thread might suggests where and how
the ab1 format stores these data, I would be very thankful as it would
save space (why have a .scf and .ab1 file?).

   For what is worth, I have attached a gif of my subregion.  I have found
it very useful and very informative for review.



Kevin Viel
Department of Epidemiology
Rollins School of Public Health
Emory University
Atlanta, GA 30322

On Wed, 28 Apr 2004, Malay wrote:

> Here is a way to do this out of the BioPerl:
> Download and istall ABI.pm
> http://cpan.uwinnipeg.ca/cpan/authors/id/M/MA/MALAY/ABI-0.01.tar.gz
> use ABI;
> my $abi = ABI->new(-file=>"mysequence.abi");
> my $seq = $abi->get_sequence(); # To get the sequence
> my @trace_a = $abi->get_trace("A"); # Get the raw traces for "A"
> my @trace_g = $abi->get_trace("G"); # Get the raw traces for "G"
> my @base_calls = $abi->get_base_calls(); # Get the base calls
> Malay
> malay at mail.nih.gov
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