—————#
# BioPerl module for FAST::Bio::AlignIO::fasta
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the L<FAST::Bio::AlignIO>
class.
=head1 DESCRIPTION
This object can transform L<FAST::Bio::SimpleAlign> objects to and from
fasta flat file databases. This is for the fasta alignment format, not
for the FastA sequence analysis program. To process the alignments from
FastA (FastX, FastN, FastP, tFastA, etc) use the FAST::Bio::SearchIO module.
=head1 FEEDBACK
=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
Peter Schattner
=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::AlignIO::fasta;
use
strict;
our
$WIDTH
= 60;
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln
Function: returns the next alignment in the stream.
Returns : FAST::Bio::Align::AlignI object - returns 0 on end of file
or on error
Args : -width => optional argument to specify the width sequence
will be written (60 chars by default)
See L<FAST::Bio::Align::AlignI>
=cut
sub
next_aln {
my
$self
=
shift
;
my
(
$width
) =
$self
->_rearrange([
qw(WIDTH)
],
@_
);
$self
->width(
$width
||
$WIDTH
);
my
(
$start
,
$end
,
$name
,
$seqname
,
$seq
,
$seqchar
,
$entry
,
$tempname
,
$tempdesc
,
%align
,
$desc
,
$maxlen
);
my
$aln
= FAST::Bio::SimpleAlign->new();
while
(
defined
(
$entry
=
$self
->_readline) ) {
chomp
$entry
;
if
(
$entry
=~ s/^>\s*(\S+)\s*// ) {
$tempname
= $1;
chomp
(
$entry
);
$tempdesc
=
$entry
;
if
(
defined
$name
) {
$seqchar
=~ s/\s//g;
# put away last name and sequence
if
(
$name
=~ /(\S+)\/(\d+)-(\d+)/ ) {
$seqname
= $1;
$start
= $2;
$end
= $3;
}
else
{
$seqname
=
$name
;
$start
= 1;
$end
=
$self
->_get_len(
$seqchar
);
}
$seq
= FAST::Bio::LocatableSeq->new
(
'-seq'
=>
$seqchar
,
'-display_id'
=>
$seqname
,
'-description'
=>
$desc
,
'-start'
=>
$start
,
'-end'
=>
$end
,
'-alphabet'
=>
$self
->alphabet,
);
$aln
->add_seq(
$seq
);
$self
->debug(
"Reading $seqname\n"
);
}
$desc
=
$tempdesc
;
$name
=
$tempname
;
$desc
=
$entry
;
$seqchar
=
""
;
next
;
}
# removed redundant symbol validation
# this is already done in FAST::Bio::PrimarySeq
$seqchar
.=
$entry
;
}
# Next two lines are to silence warnings that
# otherwise occur at EOF when using <$fh>
$name
=
""
if
(!
defined
$name
);
$seqchar
=
""
if
(!
defined
$seqchar
);
$seqchar
=~ s/\s//g;
# Put away last name and sequence
if
(
$name
=~ /(\S+)\/(\d+)-(\d+)/ ) {
$seqname
= $1;
$start
= $2;
$end
= $3;
}
else
{
$seqname
=
$name
;
$start
= 1;
$end
=
$self
->_get_len(
$seqchar
);
}
# This logic now also reads empty lines at the
# end of the file. Skip this is seqchar and seqname is null
unless
(
length
(
$seqchar
) == 0 &&
length
(
$seqname
) == 0 ) {
$seq
= FAST::Bio::LocatableSeq->new
(
'-seq'
=>
$seqchar
,
'-display_id'
=>
$seqname
,
'-description'
=>
$desc
,
'-start'
=>
$start
,
'-end'
=>
$end
,
'-alphabet'
=>
$self
->alphabet,
);
$aln
->add_seq(
$seq
);
$self
->debug(
"Reading $seqname\n"
);
}
my
$alnlen
=
$aln
->
length
;
foreach
my
$seq
(
$aln
->each_seq ) {
if
(
$seq
->
length
<
$alnlen
) {
my
(
$diff
) = (
$alnlen
-
$seq
->
length
);
$seq
->seq(
$seq
->seq() .
"-"
x
$diff
);
}
}
# no sequences means empty alignment (possible EOF)
return
$aln
if
$aln
->num_sequences;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in fasta format
Returns : 1 for success and 0 for error
Args : L<FAST::Bio::Align::AlignI> object
See L<FAST::Bio::Align::AlignI>
=cut
sub
write_aln {
my
(
$self
,
@aln
) =
@_
;
my
$width
=
$self
->width;
my
(
$seq
,
$desc
,
$rseq
,
$name
,
$count
,
$length
,
$seqsub
);
foreach
my
$aln
(
@aln
) {
if
( !
$aln
|| !
$aln
->isa(
'FAST::Bio::Align::AlignI'
) ) {
$self
->
warn
(
"Must provide a FAST::Bio::Align::AlignI object when calling write_aln"
);
next
;
}
if
(
$self
->force_displayname_flat ) {
$aln
->set_displayname_flat(1);
}
foreach
$rseq
(
$aln
->each_seq() ) {
$name
=
$aln
->displayname(
$rseq
->get_nse());
$seq
=
$rseq
->seq();
$desc
=
$rseq
->description ||
''
;
$desc
=
' '
.
$desc
if
$desc
;
$self
->_print (
">$name$desc\n"
) or
return
;
$count
= 0;
$length
=
length
(
$seq
);
if
(
defined
$seq
&&
$length
> 0) {
$seq
=~ s/(.{1,
$width
})/$1\n/g;
}
else
{
$seq
=
"\n"
;
}
$self
->_print(
$seq
);
}
}
$self
->flush
if
$self
->_flush_on_write &&
defined
$self
->_fh;
return
1;
}
=head2 _get_len
Title : _get_len
Usage :
Function: determine number of alphabetic chars
Returns : integer
Args : sequence string
=cut
sub
_get_len {
my
(
$self
,
$seq
) =
@_
;
my
$chars
=
$FAST::Bio::LocatableSeq::RESIDUE_SYMBOLS
;
$seq
=~ s{[^
$chars
]+}{}gi;
return
CORE::
length
(
$seq
);
}
=head2 width
Title : width
Usage : $obj->width($newwidth)
$width = $obj->width;
Function: Get/set width of alignment
Returns : integer value of width
Args : on set, new value (a scalar or undef, optional)
=cut
sub
width{
my
$self
=
shift
;
return
$self
->{
'_width'
} =
shift
if
@_
;
return
$self
->{
'_width'
} ||
$WIDTH
;
}
1;