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

SRMD, Col - Underwood, Anthony Anthony.Underwood at hpa.org.uk
Fri Mar 19 10:37:27 EST 2004

Hi Kevin

As far as I am aware the ABI module doesn't allow this. However if you run
an abi file through phred (available free to
academic/non-profit-http://www.phrap.org/) with the -c option (e.g phred -c
trace.abi) this will write out an scf file which can have the trace values
extracted using the BioPerl SCF IO module. I hope that this helps.


Dr Anthony Underwood
Bioinformatics Group
Genomics, Proteomic and Bioinformatics Unit
Central Public Health Laboratory
Health Protection Agency
61 Colindale Avenue
t:    0208 2004400 ext. 3618
f:    0208 3583138
e: anthony.underwood at hpa.org.uk

> -----Original Message-----
> From: Kevin Roland Viel [mailto:kviel at emory.edu]
> Sent: 19 March 2004 14:49
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] ABI.pm and .ab1 files
> Is it possible to use the ABI.pm module to abstract the trace 
> values from
> *.ab1 files?  My inclination is that is not possible.  
> Admittedly, I am
> quite weak in perl.  Examining the module, I see only that it uses the
> binmode() function.  I do not have an example of an *.abi file, but I
> cannot see where ABI.pm treats the file as anything different 
> from a text
> file.  I understand that the .ab1 file stores its data in Big Endian
> format.  It could be that IO::File incorporates this, however.
> Thanks in advance,
> Kevin
> Kevin Viel
> Department of Epidemiology
> Rollins School of Public Health
> Emory University
> Atlanta, GA 30322
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