————————#
# BioPerl module for FAST::Bio::Search::Result::HmmpfamResult
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::Search::Result::HmmpfamResult - A parser and result object for hmmpfam
results
=head1 SYNOPSIS
# generally we use FAST::Bio::SearchIO to build these objects
use FAST::Bio::SearchIO;
my $in = FAST::Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.hmmer');
while (my $result = $in->next_result) {
print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
}
=head1 DESCRIPTION
This object implements a parser for hmmpfam result output, a program in the HMMER
package.
=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
the Bioperl mailing list. 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
of the bugs and their resolution. Bug reports can be submitted via the
web:
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.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...
use
strict;
=head2 new
Title : new
Usage : my $obj = FAST::Bio::SearchIO::Result::hmmpfam->new();
Function: Builds a new FAST::Bio::SearchIO::Result::hmmpfam object
Returns : FAST::Bio::SearchIO::Result::hmmpfam
Args : -chunk => [FAST::Bio::Root::IO, $start, $end] (required if no -parent)
-parent => FAST::Bio::PullParserI object (required if no -chunk)
-parameters => hash ref of search parameters (key => value), optional
-statistics => hash ref of search statistics (key => value), optional
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
result, and $start and $end define the tell() position within the
filehandle that the result data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
=cut
sub
new {
my
(
$class
,
@args
) =
@_
;
my
$self
=
$class
->SUPER::new(
@args
);
$self
->_setup(
@args
);
foreach
my
$field
(
qw( header hit_table hsp_table alignments next_model models query_length )
) {
$self
->_fields->{
$field
} =
undef
;
}
$self
->_dependencies( { (
query_name
=>
'header'
,
query_accession
=>
'header'
,
query_description
=>
'header'
,
hit_table
=>
'header'
,
num_hits
=>
'hit_table'
,
no_hits_found
=>
'hit_table'
,
hsp_table
=>
'hit_table'
,
next_alignment
=>
'hsp_table'
) } );
return
$self
;
}
#
# PullParserI discovery methods so we can answer all ResultI questions
#
sub
_discover_header {
my
$self
=
shift
;
$self
->_chunk_seek(0);
my
$header
=
$self
->_get_chunk_by_end(
"all domains):\n"
);
$self
->{_after_header} =
$self
->_chunk_tell;
$header
||
$self
->throw(
"Could not find hmmer header, is file really hmmer format?"
);
(
$self
->_fields->{query_name}) =
$header
=~ /^Query(?:\s+sequence)?:\s+(\S+)/m;
(
$self
->_fields->{query_accession}) =
$header
=~ /^Accession:\s+(\S+)/m;
(
$self
->_fields->{query_description}) =
$header
=~ /^Description:\s+(\S.+)/m;
$self
->_fields->{query_accession} ||=
''
;
$self
->_fields->{query_description} ||=
''
;
$self
->_fields->{header} = 1;
# stop this method being called again
}
sub
_discover_hit_table {
my
$self
=
shift
;
$self
->_chunk_seek(
$self
->{_after_header});
my
$table
=
$self
->_get_chunk_by_end(
"for domains:\n"
);
$self
->{_after_hit_table} =
$self
->_chunk_tell;
my
$evalue_cutoff
=
$self
->get_field(
'evalue_cutoff'
);
undef
$evalue_cutoff
if
$evalue_cutoff
eq
'[unset]'
;
my
$score_cutoff
=
$self
->get_field(
'score_cutoff'
);
undef
$score_cutoff
if
$score_cutoff
eq
'[unset]'
;
my
$hsps_cutoff
=
$self
->get_field(
'hsps_cutoff'
);
undef
$hsps_cutoff
if
$hsps_cutoff
eq
'[unset]'
;
my
@table
;
my
$no_hit
= 1;
while
(
$table
=~ /^(\S+)\s+(\S.+?)?\s+(\S+)\s+(\S+)\s+(\d+)\n/gm) {
$no_hit
= 0;
my
$evalue
=
abs
($4);
# consistency for tests under Windows
next
if
(
$evalue_cutoff
&&
$evalue
>
$evalue_cutoff
);
next
if
(
$score_cutoff
&& $3 <
$score_cutoff
);
next
if
(
$hsps_cutoff
&& $5 <
$hsps_cutoff
);
push
(
@table
, [$1, $2, $3,
$evalue
, $5]);
}
$self
->_fields->{hit_table} = \
@table
;
$self
->{_next_hit_index} =
@table
> 0 ? 0 : -1;
$self
->_fields->{no_hits_found} =
$no_hit
;
$self
->_fields->{num_hits} =
@table
;
}
sub
_discover_hsp_table {
my
$self
=
shift
;
$self
->_chunk_seek(
$self
->{_after_hit_table});
my
$table
=
$self
->_get_chunk_by_end(
"top-scoring domains:\n"
);
$table
||=
$self
->_get_chunk_by_end(
"//\n"
);
# A0 reports
$self
->{_after_hsp_table} =
$self
->_chunk_tell;
my
%table
;
# can't save this regex work for the hsp object because the hit object needs
# its length, so may as well just do all the work here
while
(
$table
=~ /^(\S+)\s+(\d+)\/\d+\s+(\d+)\s+(\d+)\s+\S\S\s+(\d+)\s+(\d+)\s+\S(\S)\s+(\S+)\s+(\S+)/gm) {
# rank query_start query_end hit_start hit_end score evalue
my
$evalue
=
abs
($9);
# consistency for tests under Windows
push
(@{
$table
{$1}->{hsp_data}}, [$2, $3, $4, $5, $6, $8,
$evalue
]);
if
($7 eq
']'
) {
$table
{$1}->{hit_length} = $6;
}
}
$self
->_fields->{hsp_table} = \
%table
;
}
sub
_discover_alignments {
my
$self
=
shift
;
$self
->_fields->{alignments} = { };
}
sub
_next_alignment {
my
$self
=
shift
;;
return
if
$self
->{_no_more_alignments};
my
$aligns
=
$self
->_fields->{alignments};
unless
(
defined
$self
->{_after_previous_alignment}) {
$self
->_chunk_seek(
$self
->{_after_hsp_table});
my
$chunk
=
$self
->_get_chunk_by_end(
": domain"
);
unless
(
$chunk
) {
$self
->{_no_more_alignments} = 1;
return
;
}
$self
->{_after_previous_alignment} =
$self
->_chunk_tell;
$self
->{_next_alignment_start_text} =
$chunk
;
return
$self
->_next_alignment;
}
$self
->_chunk_seek(
$self
->{_after_previous_alignment});
my
$chunk
=
$self
->_get_chunk_by_end(
": domain"
);
unless
(
$chunk
) {
$self
->_chunk_seek(
$self
->{_after_previous_alignment});
$chunk
=
$self
->_get_chunk_by_end(
"//"
);
unless
(
$chunk
) {
$self
->{_no_more_alignments} = 1;
return
;
}
}
$self
->{_after_previous_alignment} =
$self
->_chunk_tell;
if
(
defined
$self
->{_next_alignment_start_text}) {
$chunk
=
$self
->{_next_alignment_start_text}.
$chunk
;
}
$chunk
=~ s/(\S+: domain)$//;
$self
->{_next_alignment_start_text} = $1;
my
(
$name
,
$domain
) =
$chunk
=~ /^(\S+): domain (\d+)/;
$aligns
->{
$name
.
'~~~~'
.
$domain
} =
$chunk
;
return
1;
}
sub
_discover_next_hit {
my
$self
=
shift
;
my
@hit_table
= @{
$self
->get_field(
'hit_table'
)};
return
if
$self
->{_next_hit_index} == -1;
#[name description score significance num_hsps rank]
my
@hit_data
= (@{
$hit_table
[
$self
->{_next_hit_index}++]},
$self
->{_next_hit_index});
$self
->_fields->{next_hit} = FAST::Bio::Search::Hit::HmmpfamHit->new(
-parent
=>
$self
,
-hit_data
=> \
@hit_data
);
if
(
$self
->{_next_hit_index} >
$#hit_table
) {
$self
->{_next_hit_index} = -1;
}
}
=head2 next_hit
Title : next_hit
Usage : while( $hit = $result->next_hit()) { ... }
Function: Returns the next available Hit object, representing potential
matches between the query and various entities from the database.
Returns : a FAST::Bio::Search::Hit::HitI object or undef if there are no more.
Args : none
=cut
sub
next_hit {
my
$self
=
shift
;
my
$hit
=
$self
->get_field(
'next_hit'
);
undef
$self
->_fields->{next_hit};
return
$hit
;
}
=head2 next_model
Title : next_model
Usage : my $domain = $result->next_model
Function: Returns the next domain - this is an alias for next_hit()
Returns : L<FAST::Bio::Search::Hit::HitI> object
Args : none
=cut
*next_model
= \
&next_hit
;
=head2 hits
Title : hits
Usage : my @hits = $result->hits
Function: Returns the HitI objects contained within this Result
Returns : Array of FAST::Bio::Search::Hit::HitI objects
Args : none
See Also: L<FAST::Bio::Search::Hit::HitI>
=cut
sub
hits {
my
$self
=
shift
;
my
$old
=
$self
->{_next_hit_index} || 0;
$self
->rewind;
my
@hits
;
while
(
defined
(
my
$hit
=
$self
->next_hit)) {
push
(
@hits
,
$hit
);
}
$self
->{_next_hit_index} =
@hits
> 0 ?
$old
: -1;
return
@hits
;
}
=head2 models
Title : models
Usage : my @domains = $result->models;
Function: Returns the list of HMM models seen - this is an alias for hits()
Returns : Array of L<FAST::Bio::Search::Hit::HitI> objects
Args : none
=cut
*models
= \
&hits
;
=head2 sort_hits
Title : sort_hits
Usage : $result->sort_hits('<score')
Function : Sorts the hits so that they come out in the desired order when
hits() or next_hit() is called.
Returns : n/a
Args : A coderef for the sort function. See the documentation on the Perl
sort() function for guidelines on writing sort functions.
You will be sorting array references, not HitI objects. The
references contain name as element 0, description as element 1,
score as element 2, significance as element 3 and number of hsps
as element 4.
By default the sort order is ascending significance value (ie.
most significant hits first).
Note : To access the special variables $a and $b used by the Perl sort()
function the user function must access
FAST::Bio::Search::Result::HmmpfamResult namespace.
For example, use :
$result->sort_hits(
sub{$FAST::Bio::Search::Result::HmmpfamResult::a->[2]
<=>
$FAST::Bio::Search::Result::HmmpfamResult::b->[2]});
NOT $result->sort_hits($a->[2] <=> $b->[2]);
=cut
sub
sort_hits {
my
(
$self
,
$code_ref
) =
@_
;
$code_ref
||=
sub
{
$a
->[3] <=>
$b
->[3] };
# avoid creating hit objects just to sort, hence force user to sort on
# the array references in hit table
my
$table_ref
=
$self
->get_field(
'hit_table'
);
@{
$table_ref
} > 1 ||
return
;
my
@sorted
=
sort
$code_ref
@{
$table_ref
};
@sorted
== @{
$table_ref
} ||
$self
->throw(
"Your sort routine failed to give back all hits!"
);
$self
->_fields->{hit_table} = \
@sorted
;
}
=head2 rewind
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iterator to the beginning, so that
next_hit() will subsequently return the first hit and so on.
Returns : n/a
Args : none
=cut
sub
rewind {
my
$self
=
shift
;
unless
(
$self
->_fields->{hit_table}) {
$self
->get_field(
'hit_table'
);
}
$self
->{_next_hit_index} = @{
$self
->_fields->{hit_table}} > 0 ? 0 : -1;
}
1;