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Import Bio::SeqIO abi, alf, ctf, exp, pln, and ztr
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Imported from bioperl-live c98b3b5ccff668d55a05bf9516f172a1a5be946c

Only adapted the tests.  The test data files in bioperl-live are the
same data files already in this repo, only had a different name.

The tests for alf.t try to make use of a test.alf that didn't exist
in bioperl-live and also does not exist here in bioperl-ext.
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carandraug committed Sep 24, 2018
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188 changes: 188 additions & 0 deletions Bio/SeqIO/abi.pm
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# BioPerl module for Bio::SeqIO::abi
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Aaron Mackey <amackey@virginia.edu>
#
# Copyright Aaron Mackey
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME
Bio::SeqIO::abi - abi trace sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from abi trace
files. To optionally read the trace graph data (which can be used
to draw chromatographs, for instance), set the optional
'-get_trace_data' flag or the get_trace_data method to a value
evaluating to TRUE.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHORS - Aaron Mackey
Email: amackey@virginia.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut

# Let the code begin...

package Bio::SeqIO::abi;
use vars qw(@ISA $READ_AVAIL);
use strict;

use Bio::SeqIO;
use Bio::Seq::SeqFactory;

push @ISA, qw( Bio::SeqIO );

sub BEGIN {
eval { require Bio::SeqIO::staden::read; };
if ($@) {
$READ_AVAIL = 0;
} else {
push @ISA, "Bio::SeqIO::staden::read";
$READ_AVAIL = 1;
}
}

sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($get_trace) = $self->_rearrange([qw(get_trace_data)],@args);
$get_trace && $self->get_trace_data(1);
if( ! defined $self->sequence_factory ) {
$self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality'));
}
unless ($READ_AVAIL) {
Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
-text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
);
}
}

=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq::Quality object
Args : NONE
=cut

sub next_seq {

my ($self) = @_;

my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'abi');

# create the seq object
my ($base_locs, $a_trace, $c_trace, $g_trace, $t_trace, $points, $max_height);
if ($self->get_trace_data) {
($base_locs, $a_trace, $c_trace, $g_trace, $t_trace, $points, $max_height) = $self->read_trace_with_graph($self->_fh, 'abi');
} else {
$base_locs = [];
}

# create the seq object
$seq = $self->sequence_factory->create(-seq => $seq,
-id => $id,
-primary_id => $id,
-desc => $desc,
-alphabet => 'DNA',
-qual => $qual,
-trace => join (" ", @{$base_locs}),
-trace_data => { a_trace => $a_trace,
c_trace => $c_trace,
g_trace => $g_trace,
t_trace => $t_trace,
max_height => $max_height,
num_points => $points }
);
return $seq;
}

=head2 write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
=cut

sub write_seq {
my ($self,@seq) = @_;

my $fh = $self->_fh;
foreach my $seq (@seq) {
$self->write_trace($fh, $seq, 'abi');
}

$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}

=head2 get_trace_data
Title : get_trace_data
Usage : $stream->get_trace_data(1)
Function: set boolean flag to retrieve the trace data (possibly for
output)
Returns : bool value, TRUE = retrieve trace data (default FALSE)
Args : bool value
=cut

sub get_trace_data {
my ($self, $val) = @_;
$self->{_get_trace_data} = $val ? 1 : 0 if (defined $val);
$self->{_get_trace_data};
}

1;
151 changes: 151 additions & 0 deletions Bio/SeqIO/alf.pm
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# BioPerl module for Bio::SeqIO::alf
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Aaron Mackey <amackey@virginia.edu>
#
# Copyright Aaron Mackey
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME
Bio::SeqIO::alf - alf trace sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from alf trace
files.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHORS - Aaron Mackey
Email: amackey@virginia.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut

# Let the code begin...

package Bio::SeqIO::alf;
use vars qw(@ISA $READ_AVAIL);
use strict;

use Bio::SeqIO;
use Bio::Seq::SeqFactory;

push @ISA, qw( Bio::SeqIO );

sub BEGIN {
eval { require Bio::SeqIO::staden::read; };
if ($@) {
$READ_AVAIL = 0;
} else {
push @ISA, "Bio::SeqIO::staden::read";
$READ_AVAIL = 1;
}
}

sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
if( ! defined $self->sequence_factory ) {
$self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::Seq::Quality'));
}
unless ($READ_AVAIL) {
Bio::Root::Root->throw( -class => 'Bio::Root::SystemException',
-text => "Bio::SeqIO::staden::read is not available; make sure the bioperl-ext package has been installed successfully!"
);
}
}

=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq::Quality object
Args : NONE
=cut

sub next_seq {

my ($self) = @_;

my ($seq, $id, $desc, $qual) = $self->read_trace($self->_fh, 'alf');

# create the seq object
$seq = $self->sequence_factory->create(-seq => $seq,
-id => $id,
-primary_id => $id,
-desc => $desc,
-alphabet => 'DNA',
-qual => $qual
);
return $seq;
}

=head2 write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
=cut

sub write_seq {
my ($self,@seq) = @_;

my $fh = $self->_fh;
foreach my $seq (@seq) {
$self->write_trace($fh, $seq, 'alf');
}

$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}

1;

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