—————#
# BioPerl module for FAST::Bio::SeqIO::gcg
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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
FAST::Bio::SeqIO::gcg - GCG sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the FAST::Bio::SeqIO class.
=head1 DESCRIPTION
This object can transform FAST::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://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:
=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
FAST::Bio::SeqIO::gcg;
use
strict;
sub
_initialize {
my
(
$self
,
@args
) =
@_
;
$self
->SUPER::_initialize(
@args
);
if
( !
defined
$self
->sequence_factory ) {
$self
->sequence_factory(FAST::Bio::Seq::SeqFactory->new
(
-verbose
=>
$self
->verbose(),
-type
=>
'FAST::Bio::Seq::RichSeq'
));
}
}
=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : FAST::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/[\d\s\t]//g;
## remove anything that is not alphabet char: preserve anything that is not explicitly specified for removal (Stefan Kirov)
# $_ = uc($_); ## 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(
uc
(
$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 FAST::Bio::PrimarySeqI object
=cut
sub
write_seq {
my
(
$self
,
@seq
) =
@_
;
for
my
$seq
(
@seq
) {
$self
->throw(
"Did not provide a valid FAST::Bio::PrimarySeqI object"
)
unless
defined
$seq
&&
ref
(
$seq
) &&
$seq
->isa(
'FAST::Bio::PrimarySeqI'
);
$self
->
warn
(
"No whitespace allowed in GCG ID ["
.
$seq
->display_id.
"]"
)
if
$seq
->display_id =~ /\s/;
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 FAST::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;