ABI.pm - Perl module to parse chromatogram files generated by Applied Biosystems (ABI) automated DNA sequencing machine.
Please cite: ABI.pm - Perl module to parse chromatogram files generated by Applied Biosystems (ABI) automated DNA sequencing machine. by Malay K Basu (malay@bioinformatics.org); source code available at: http://search.cpan.org/~malay
Version 1.0
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
An ABI chromatogram file is in binary format. It contain several information only some of which is required for normal use. This module only gives access to the most used information stored in ABI file. All the accesses are read only.
If you have edited the file using a trace editor, then you can use the corresponding method to access the edited sequence and base calls.
Usage : $abi = ABI->new(-file=>"filename"); $abi = ABI->new("filename"); # same thing
Title : get_max_trace() Usage : $max = $abi->get_max_trace(); Function : Returns the maximum trace value of all the traces. Args : Nothing Returns : A scalar
Title : get_trace() Usage : my @a = $abi->get_trace("A"); Function : Returns the raw traces as array. Args : "A" or "G" or "C" or "T" Returns : An array
Title : get_sequence() Usage : my $seq = $abi->get_sequence(); Function : Returns the original unedited sequence as string. If you want to access the edited sequence use "get_corrected_sequence()" instead. Args : Nothing Returns : A scalar
Title : get_corrected_sequence() Usage : my $seq = $abi->get_corrected_sequence(); Function : Returns the corrected sequence as string. If you want to access the original unedited sequence, use "get_sequence()" instead. Args : Nothing Returns : A scalar
Title : get_sequence_length() Usage : my $seq_length = $abi->get_sequence_length(); Function : Returns the sequence length of the orginal unedited sequence. Args : Nothing Returns : A scalar
Title : get_corrected_sequence_length() Usage : my $seq_length = $abi->get_corrected_sequence_length(); Function : Returns the length of the edited sequence. Args : Nothing Returns : A scalar
Title : get_trace_length() Usage : my $trace_length = $abi->get_trace_length(); Function : Returns the trace length Args : Nothing Returns : A scalar
Title : get_base_calls() Usage : my @base_calls = $abi->get_base_calls(); Function : Returns the called bases by the base caller. This method will return the unedited original basecalls created by the basecaller. Args : Nothing Returns : An array
Title : get_corrected_base_calls() Usage : my @base_calls = $abi->get_corrected_base_calls(); Function : If you have edited the trace file you can get the corrected base call with this method Args : Nothing Returns : An array
Title : get_sample_name() Usage : my $sample = $abi->get_sample_name(); Function : Returns hard coded sample name Args : Nothing Returns : A scalar
Malay <malay@bioinformatics.org>
Please report any bugs or feature requests to bug-abi at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=ABI. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-abi at rt.cpan.org
or
You can directly contact me to my email address.
You can find documentation for this module with the perldoc command.
perldoc ABI
You can also look for information at:
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/ABI
CPAN Ratings
http://cpanratings.perl.org/d/ABI
RT: CPAN's request tracker
http://rt.cpan.org/NoAuth/Bugs.html?Dist=ABI
Search CPAN
http://search.cpan.org/dist/ABI
Copyright 2002,2006 Malay, all rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
To install ABI, copy and paste the appropriate command in to your terminal.
cpanm
cpanm ABI
CPAN shell
perl -MCPAN -e shell install ABI
For more information on module installation, please visit the detailed CPAN module installation guide.