/usr/share/perl5/Bio/SeqIO/alf.pm is in libbio-perl-perl 1.6.924-3.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 | # 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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