NAME
ABI.pm - Perl module to parse chromatogram files generated by Applied Biosystems (ABI) automated DNA sequencing machine.
SYNOPSIS
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 callsDESCRIPTION
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.
FEEDBACK
Malay <curiouser@gene.ccmbindia.org>
CONSTRUCTOR
new()
Usage : $abi = ABI->new(-file=>"filename");
$abi = ABI->new("filename"); # same thingMETHODS
get_max_trace()
Title : get_max_trace()
Usage : $max = $abi->get_max_trace();
Function : Returns the maximum trace value of all the traces.
Args : Nothing
Returns : A scalarget_trace()
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 arrayget_sequence()
Title : get_sequence()
Usage : my $seq = $abi->get_sequence();
Function : Returns the sequence as string
Args : Nothing
Returns : A scalarget_sequence_length()
Title : get_sequence_length()
Usage : my $seq_length = $abi->get_sequence_length();
Function : Returns the sequence length
Args : Nothing
Returns : A scalarget_trace_length()
Title : get_trace_length()
Usage : my $trace_length = $abi->get_trace_length();
Function : Returns the trace length
Args : Nothing
Returns : A scalarget_base_calls()
Title : get_base_calls()
Usage : my @base_calls = $abi->get_base_calls();
Function : Returns the called bases by the base caller
Args : Nothing
Returns : An arrayget_sample_name()
Title : get_sample_name()
Usage : my $sample = $abi->get_sample_name();
Function : Returns hard coded sample name
Args : Nothing
Returns : A scalar