• NAME
• SYNOPSIS
• DESCRIPTION
• FEEDBACK
• CONSTRUCTOR
• new()
• METHODS
• get_max_trace()
• get_trace()
• get_sequence()
• get_sequence_length()
• get_trace_length()
• get_base_calls()
• get_sample_name()

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 calls

DESCRIPTION

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 thing

METHODS

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 scalar

get_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 array

get_sequence()

  Title    : get_sequence()
  Usage    : my $seq = $abi->get_sequence();
  Function : Returns the sequence as string
  Args     : Nothing
  Returns  : A scalar

get_sequence_length()

  Title    : get_sequence_length()
  Usage    : my $seq_length = $abi->get_sequence_length();
  Function : Returns the sequence length 
  Args     : Nothing
  Returns  : A scalar

get_trace_length()

  Title    : get_trace_length()
  Usage    : my $trace_length = $abi->get_trace_length();
  Function : Returns the trace length
  Args     : Nothing
  Returns  : A scalar

get_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 array

get_sample_name()

  Title    : get_sample_name()
  Usage    : my $sample = $abi->get_sample_name();
  Function : Returns hard coded sample name
  Args     : Nothing
  Returns  : A scalar