————# $Id: IO.pm,v 1.11.4.1 2006/10/02 23:10:13 sendu Exp $
#
# BioPerl module for Bio::CodonUsage::IO
#
# Cared for by Richard Adams (richard.adams@ed.ac.uk)
#
# Copyright Richard Adams
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::CodonUsage::IO - for reading and writing codon usage tables to file
=head1 SYNOPSIS
use Bio::CodonUsage::IO;
## read in a codon usage file
my $io = Bio::CodonUsage::IO->new(-file => "in");
my $cut = $io->next_data();
## write it out again
my $out = Bio::CodonUsage::IO->new(-file => ">out");
$out->write_data($cut);
=head1 DESCRIPTION
This class provides standard IO methods for reading and writing text files
of codon usage tables. These tables can initially be retrieved using
Bio::DB::CUTG. At present only this format is supported for read/write.
Reading a CUTG will return a Bio::CodonUsage::Table object.
=head1 SEE ALSO
L<Bio::Tools::CodonTable>,
L<Bio::WebAgent>,
L<Bio::CodonUsage::Table>,
L<Bio::CodonUsage::IO>
=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 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
Richard Adams, Richard.Adams@ed.ac.uk
=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::CodonUsage::IO;
=head2 new
Title : new
Usage : my $io = Bio::CodonUsage::IO->new(-file => "CUTfile");
Purpose: To read/write a Bio:CodonUsage::Table object
Returns: A Bio:CodonUsage::IO object
Args : a file or file handle
=cut
sub
new {
my
(
$class
,
@args
) =
@_
;
my
$self
=
$class
->SUPER::new(
@args
);
}
=head2 next_data
Title : next_data
Usage : my $cut = $io->next_data();
Purpose: To obtain a Bio:CodonUsage::Table object
Returns: A Bio:CodonUsage::Table object
Args : none
=cut
sub
next_data {
my
$self
=
shift
;
my
$cut
=
$self
->_parse;
return
$cut
;
}
=head2 write_data
Title : write_data
Usage : $io->write_data($cut);
Purpose: To write a CUT to file
Returns: void
Args : a Bio::CodonUsage::Table object reference
=cut
sub
write_data {
my
(
$self
,
$cut
) =
@_
;
if
(!
$cut
|| !
$cut
->isa(Bio::CodonUsage::Table)) {
$self
->throw(
"must supply a Bio::CodonUsage::Table object for writing\n"
);
}
my
$outstring
=
"Codon usage table\n\n"
;
my
$sp_string
=
$cut
->species .
"["
.
$cut
->_gb_db .
"] "
.
$cut
->cds_count .
" CDS's\n\n"
;
$outstring
.=
$sp_string
;
my
$colhead
=
sprintf
(
"%-9s%-9s%15s%12s%12s\n\n"
,
"AmAcid"
,
"Codon"
,
"Number"
,
"/1000"
,
"Fraction"
);
$outstring
.=
$colhead
;
### now write bulk of codon data ##
my
$ctable
= Bio::Tools::CodonTable->new;
for
my
$f
(
qw(G A T C)
) {
for
my
$s
(
qw(G A T C)
) {
for
my
$t
(
qw(G A T C)
) {
$cod
=
$f
.
$s
.
$t
;
my
$aa
=
$Bio::SeqUtils::THREECODE
{
$ctable
->translate(
$cod
)};
my
$codstr
=
sprintf
(
"%-9s%-9s%15.2f%12.2f%12.2f\n"
,
$aa
,
$cod
,
my
$tt
=
$cut
->codon_count(
$cod
)|| 0.00,
my
$ll
=
$cut
->{
'_table'
}{
$aa
}{
$cod
}{
'per1000'
}|| 0.00,
my
$ss
=
$cut
->codon_rel_frequency(
$cod
) || 0.00);
$outstring
.=
$codstr
;
}
$outstring
.=
"\n"
;
}
}
$outstring
.=
"\n\n"
;
## now append GC data
$outstring
.=
"Coding GC "
.
$cut
->get_coding_gc(
'all'
).
"%\n"
;
$outstring
.=
"1st letter GC "
.
$cut
->get_coding_gc(1).
"%\n"
;
$outstring
.=
"2nd letter GC "
.
$cut
->get_coding_gc(2).
"%\n"
;
$outstring
.=
"3rd letter GC "
.
$cut
->get_coding_gc(3).
"%\n"
;
$outstring
.=
"Genetic code "
.
$cut
->genetic_code() .
"\n\n\n"
;
$self
->_print (
$outstring
);
$self
->flush();
}
sub
_parse {
my
$self
=
shift
;
my
$cdtableobj
= Bio::CodonUsage::Table->new();
while
(
my
$line
=
$self
->_readline() ) {
next
if
$line
=~ /^$/ ;
$line
=~ s/End/Ter/;
## now parse in species name, cds number
if
(
$line
=~ /^(.+?)\s*\[(\w+)\].+?(\d+)/) {
$cdtableobj
->species($1);
$cdtableobj
->{
'_gb_db'
} = $2;
$cdtableobj
->cds_count($3);
}
## now parse in bulk of codon usage table
elsif
(
$line
=~ /^(\w\w\w)\s+(\w+)\s+(\d+\.\d+)
\s+(\d+\.\d+)\s+(\d+\.\d+)/x){
if
(
defined
($1)) {
$cdtableobj
->{
'_table'
}{$1}{$2} = {
'abs_count'
=>$3,
'per1000'
=> $4,
'rel_freq'
=> $5,
};
}
}
## now parse in gc data ####
if
(
$line
=~ /^Cod.+?(\d\d\.\d\d)/ ){
$cdtableobj
->{
'_coding_gc'
}{
'all'
} = $1;
}
elsif
(
$line
=~ /^1st.+?(\d\d\.\d\d)/){
$cdtableobj
->{
'_coding_gc'
}{
'1'
} = $1;
}
elsif
(
$line
=~ /^2nd.+?(\d\d\.\d\d)/){
$cdtableobj
->{
'_coding_gc'
}{
'2'
} = $1;
}
elsif
(
$line
=~ /^3rd.+?(\d\d\.\d\d)/){
$cdtableobj
->{
'_coding_gc'
}{
'3'
} = $1;
}
elsif
(
$line
=~ /^Gen.+?(\d+)/){
$cdtableobj
->{
'_genetic_code'
} = $1;
}
}
## check has been parsed ok ##
if
(
scalar
keys
%{
$cdtableobj
->{
'_table'
}} != 21) {
$cdtableobj
->
warn
(
"probable parsing error - should be 21 entries for 20aa + stop codon"
);
}
return
$cdtableobj
;
}
1;
__END__