Raw content of Bio::SeqIO::gcg
<![CDATA[# $Id: gcg.pm,v 1.21 2002/10/25 16:22:01 jason Exp $
#
# BioPerl module for Bio::SeqIO::gcg
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# Copyright Ewan Birney & Lincoln Stein
#
# You may distribute this module under the same terms as perl itself
#
# _history
# October 18, 1999 Largely rewritten by Lincoln Stein
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::gcg - GCG 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 GCG flat
file databases.
=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://www.bioperl.org/MailList.shtml - About the mailing lists
=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 email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHORS - Ewan Birney & Lincoln Stein
Email: E<lt>birney@ebi.ac.ukE<gt>
E<lt>lstein@cshl.orgE<gt>
=head1 CONTRIBUTORS
Jason Stajich, jason@bioperl.org
=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::gcg;
use vars qw(@ISA);
use strict;
use Bio::SeqIO;
use Bio::Seq::SeqFactory;
@ISA = qw(Bio::SeqIO);
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
if( ! defined $self->sequence_factory ) {
$self->sequence_factory(new Bio::Seq::SeqFactory
(-verbose => $self->verbose(),
-type => 'Bio::Seq::RichSeq'));
}
}
=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :
=cut
sub next_seq {
my ($self,@args) = @_;
my($id,$type,$desc,$line,$chksum,$sequence,$date,$len);
while( defined($_ = $self->_readline()) ) {
## Get the descriptive info (anything before the line with '..')
unless( /\.\.$/ ) { $desc.= $_; }
## Pull ID, Checksum & Type from the line containing '..'
/\.\.$/ && do { $line = $_; chomp;
if(/Check\:\s(\d+)\s/) { $chksum = $1; }
if(/Type:\s(\w)\s/) { $type = $1; }
if(/(\S+)\s+Length/)
{ $id = $1; }
if(/Length:\s+(\d+)\s+(\S.+\S)\s+Type/ )
{ $len = $1; $date = $2;}
last;
}
}
return if ( !defined $_);
chomp($desc); # remove last "\n"
while( defined($_ = $self->_readline()) ) {
## This is where we grab the sequence info.
if( /\.\.$/ ) {
$self->throw("Looks like start of another sequence. See documentation. ");
}
next if($_ eq "\n"); ## skip whitespace lines in formatted seq
s/[^a-zA-Z]//g; ## remove anything that is not alphabet char
# $_ = uc($_); ## uppercase sequence: NO. Keep the case. HL
$sequence .= $_;
}
##If we parsed out a checksum, we might as well test it
if(defined $chksum) {
unless(_validate_checksum($sequence,$chksum)) {
$self->throw("Checksum failure on parsed sequence.");
}
}
## Remove whitespace from identifier because the constructor
## will throw a warning otherwise...
if(defined $id) { $id =~ s/\s+//g;}
## Turn our parsed "Type: N" or "Type: P" (if found) into the appropriate
## keyword that the constructor expects...
if(defined $type) {
if($type eq "N") { $type = "dna"; }
if($type eq "P") { $type = "prot"; }
}
return $self->sequence_factory->create(-seq => $sequence,
-id => $id,
-desc => $desc,
-type => $type,
-dates => [ $date ]
);
}
=head2 write_seq
Title : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the formatted $seq object into the stream
Returns : 1 for success and 0 for error
Args : array of Bio::PrimarySeqI object
=cut
sub write_seq {
my ($self,@seq) = @_;
for my $seq (@seq) {
$self->throw("Did not provide a valid Bio::PrimarySeqI object")
unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
my $str = $seq->seq;
my $comment = $seq->desc;
my $id = $seq->id;
my $type = ( $seq->alphabet() =~ /[dr]na/i ) ? 'N' : 'P';
my $timestamp;
if( $seq->can('get_dates') ) {
($timestamp) = $seq->get_dates;
} else {
$timestamp = localtime(time);
}
my($sum,$offset,$len,$i,$j,$cnt,@out);
$len = length($str);
## Set the offset if we have any non-standard numbering going on
$offset=1;
# checksum
$sum = $self->GCG_checksum($seq);
#Output the sequence header info
push(@out,"$comment\n");
push(@out,"$id Length: $len $timestamp Type: $type Check: $sum ..\n\n");
#Format the sequence
$i = $#out + 1;
for($j = 0 ; $j < $len ; ) {
if( $j % 50 == 0) {
$out[$i] = sprintf("%8d ",($j+$offset)); #numbering
}
$out[$i] .= sprintf("%s",substr($str,$j,10));
$j += 10;
if( $j < $len && $j % 50 != 0 ) {
$out[$i] .= " ";
}elsif($j % 50 == 0 ) {
$out[$i++] .= "\n\n";
}
}
local($^W) = 0;
if($j % 50 != 0 ) {
$out[$i] .= "\n";
}
$out[$i] .= "\n";
return unless $self->_print(@out);
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
=head2 GCG_checksum
Title : GCG_checksum
Usage : $cksum = $gcgio->GCG_checksum($seq);
Function : returns a gcg checksum for the sequence specified
This method can also be called as a class method.
Example :
Returns : a GCG checksum string
Argument : a Bio::PrimarySeqI implementing object
=cut
sub GCG_checksum {
my ($self,$seqobj) = @_;
my $index = 0;
my $checksum = 0;
my $char;
my $seq = $seqobj->seq();
$seq =~ tr/a-z/A-Z/;
foreach $char ( split(/[\.\-]*/, $seq)) {
$index++;
$checksum += ($index * (unpack("c",$char) || 0) );
if( $index == 57 ) {
$index = 0;
}
}
return ($checksum % 10000);
}
=head2 _validate_checksum
Title : _validate_checksum
Usage : n/a - internal method
Function: if parsed gcg sequence contains a checksum field
: we compare it to a value computed here on the parsed
: sequence. A checksum mismatch would indicate some
: type of parsing failure occured.
:
Returns : 1 for success, 0 for failure
Args : string containing parsed seq, value of parsed cheksum
=cut
sub _validate_checksum {
my($seq,$parsed_sum) = @_;
my($i,$len,$computed_sum,$cnt);
$len = length($seq);
#Generate the GCG Checksum value
for($i=0; $i<$len ;$i++) {
$cnt++;
$computed_sum += $cnt * ord(substr($seq,$i,1));
($cnt == 57) && ($cnt=0);
}
$computed_sum %= 10000;
## Compare and decide if success or failure
if($parsed_sum == $computed_sum) {
return 1;
} else { return 0; }
}
1;
]]>