ABI
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=head1 CONSTRUCTOR
=head2 new()
Usage : $abi = ABI->new(-file=>"filename");
$abi = ABI->new("filename"); # same thing
=cut
sub new {
my $class = shift;
my $self = {};
bless $self, ref($class) || $class;
$self->_init(@_);
#print "****", $self->{_mac_header}, "\n";
return $self;
}
sub _init {
my ( $self, @args ) = @_;
my ($file) = $self->_rearrange( ["FILE"], @args );
if ( !defined($file) ) {
croak "Can't open the input file\n";
} else {
$self->set_file_handle($file);
}
$self->{_sequence} = "";
$self->{_sequence_corrected} = "";
$self->{_sample} = "";
$self->_set_seq();
$self->_set_corrected_seq();
$self->_set_traces();
$self->_set_max_trace();
$self->_set_sample_name();
close( $self->{_fh} );
}
return $self;
}
sub set_file_handle {
my $self = shift;
my $path = shift;
my $fh = IO::File->new();
if ( $fh->open("< $path") ) {
binmode($fh);
$self->{_fh} = $fh;
} else {
croak "Could not open $path in ABITrace::set_file_handle\n";
}
}
sub _rearrange {
my ( $self, $order, @param ) = @_;
return unless @param;
return @param unless ( defined( $param[0] ) && $param[0] =~ /^-/ );
for ( my $i = 0 ; $i < @param ; $i += 2 ) {
$param[$i] =~ s/^\-//;
$param[$i] =~ tr/a-z/A-Z/;
}
# Now we'll convert the @params variable into an associative array.
local ($^W) = 0; # prevent "odd number of elements" warning with -w.
my ($value) = $param{$key};
delete $param{$key};
push( @return_array, $value );
}
# print "\n_rearrange() after processing:\n";
# my $i; for ($i=0;$i<@return_array;$i++) { printf "%20s => %s\n", ${$order}[$i], $return_array[$i]; } <STDIN>;
return (@return_array);
}
sub _is_abi {
my $self = shift;
my $fh = $self->{"_fh"};
my $buf;
seek( $fh, 0, 0 );
read( $fh, $buf, 3 );
#my $a = unpack("n*", $buf);
if ( $buf eq "ABI" ) {
return 1;
} else {
read( $fh, $buf, 3 );
if ( $buf eq "ABI" ) {
$self->_set_mac_header();
return 1;
} else {
return 0;
}
}
}
sub _set_mac_header {
my $self = shift;
$self->{_mac_header} = 128;
}
sub _set_index {
my $self = shift;
my $data_counter = 0;
my $pbas_counter = 0;
my $ploc_counter = 0;
my ( $num_records, $buf );
#print $self->{_fh}, "\n";
#print $self->{_mac_header}, "\n";
seek( $self->{_fh}, $self->{_abs_index} + $self->{_mac_header}, 0 );
read( $self->{_fh}, $buf, 4 );
$self->{PLOC1} = $self->_get_int( $self->{PLOC1} ) + $self->{_mac_header};
$self->{DATA9} = $self->_get_int( $self->{DATA9} ) + $self->{_mac_header};
$self->{DATA10} = $self->_get_int( $self->{DATA10} ) + $self->{_mac_header};
$self->{DATA11} = $self->_get_int( $self->{DATA11} ) + $self->{_mac_header};
$self->{DATA12} = $self->_get_int( $self->{DATA12} ) + $self->{_mac_header};
$self->{PBAS1} = $self->_get_int( $self->{PBAS1} ) + $self->{_mac_header};
$self->{PBAS2} = $self->_get_int( $self->{PBAS2} ) + $self->{_mac_header};
$self->{SMPL} += $self->{_mac_header};
}
sub _set_base_calls {
my $self = shift;
my $buf;
my $length = $self->{_seq_length} * 2;
my $fh = $self->{_fh};
seek( $fh, $self->{PLOC}, 0 );
read( $fh, $buf, $length );
@{ $self->{_basecalls} } = unpack( "n" x $length, $buf );
# print "@{$self->{_basecalls}}" , "\n";
}
sub _set_corrected_base_calls {
my $self = shift;
my $buf;
my $length = $self->{_seq_length_corrected} * 2;
my $fh = $self->{_fh};
seek( $fh, $self->{PLOC1}, 0 );
read( $fh, $buf, $length );
@{ $self->{_basecalls_corrected} } = unpack( "n" x $length, $buf );
}
sub _set_seq {
my $self = shift;
my $buf;
my $length = $self->{_seq_length};
my $fh = $self->{_fh};
seek( $fh, $self->{PBAS2}, 0 );
read( $fh, $buf, $length );
$self->{_sequence} = $buf;
#my @seq = unpack( "C" x $length, $buf);
#print $buf, "\n";
}
sub _set_corrected_seq {
my $self = shift;
my $buf;
my $length = $self->{_seq_length_corrected};
my $fh = $self->{_fh};
seek( $fh, $self->{PBAS1}, 0 );
read( $fh, $buf, $length );
$self->{_sequence_corrected} = $buf;
}
sub _set_traces {
my $self = shift;
my $buf;
my ( @pointers, @A, @G, @C, @T );
my (@datas) =
( $self->{DATA9}, $self->{DATA10}, $self->{DATA11}, $self->{DATA12} );
my $fh = $self->{_fh};
seek( $fh, $self->{FWO}, 0 );
read( $fh, $buf, 4 );
my @order = split( //, $buf );
if ( $i == 3 ) {
@T = unpack( "n" x $self->{_trace_length}, $buf );
}
}
@{ $self->{A} } = @A;
@{ $self->{G} } = @G;
@{ $self->{T} } = @T;
@{ $self->{C} } = @C;
}
sub _get_int {
my $self = shift;
my $buf;
my $pos = shift;
my $fh = $self->{_fh};
seek( $fh, $pos, 0 );
read( $fh, $buf, 4 );
return unpack( "N", $buf );
}
sub _set_max_trace {
my $self = shift;
my @A = @{ $self->{A} };
my @T = @{ $self->{T} };
my @G = @{ $self->{G} };
my @C = @{ $self->{C} };
my $max = 0;
for ( my $i = 0 ; $i < @T ; $i++ ) {
if ( $T[$i] > $max ) { $max = $T[$i]; }
if ( $A[$i] > $max ) { $max = $A[$i]; }
if ( $G[$i] > $max ) { $max = $G[$i]; }
if ( $C[$i] > $max ) { $max = $C[$i]; }
}
$self->{_maximum_trace} = $max;
}
sub _set_sample_name {
my $self = shift;
my $buf;
my $fh = $self->{_fh};
seek( $fh, $self->{SMPL}, 0 );
read( $fh, $buf, 1 );
my $length = unpack( "C", $buf );
read( $fh, $buf, $length );
$self->{_sample} = $buf;
}
=head2 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
=cut
sub get_max_trace {
my $self = shift;
return $self->{_maximum_trace};
}
=head2 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
=cut
sub get_trace {
my $self = shift;
my $symbol = shift;
if ( $symbol =~ /A/i ) {
return @{ $self->{A} };
} elsif ( $symbol =~ /G/i ) {
return @{ $self->{G} };
} elsif ( $symbol =~ /C/i ) {
return @{ $self->{C} };
} elsif ( $symbol =~ /T/i ) {
return @{ $self->{T} };
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
=cut
sub get_sequence {
my $self = shift;
return $self->{_sequence};
}
=head2 get_corrected_sequence()
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
=cut
sub get_corrected_sequence {
my $self = shift;
return $self->{_sequence_corrected};
}
=head2 get_sequence_length()
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
=cut
sub get_sequence_length {
my $self = shift;
return $self->{_seq_length};
}
=head2 get_corrected_sequence_length()
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
=cut
sub get_corrected_sequence_length {
my $self = shift;
#print STDERR "**ABI**",$self->{_seq_length_corrected},"\n";
return $self->{_seq_length_corrected};
}
=head2 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
=cut
sub get_trace_length {
my $self = shift;
return $self->{_trace_length};
}
=head2 get_base_calls()
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
=cut
sub get_base_calls {
my $self = shift;
return @{ $self->{_basecalls} };
}
=head2 get_corrected_base_calls()
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
=cut
sub get_corrected_base_calls {
my $self = shift;
return @{ $self->{_basecalls_corrected} };
}
=head2 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
=cut
sub get_sample_name {
my $self = shift;
return $self->{_sample};
}
=head1 AUTHOR
Malay <malay@bioinformatics.org>
=head1 BUGS
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