Bio::SearchIO::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch)
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Code Index:
NAME
Bio::SearchIO::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch)
SYNOPSIS
# do not use this class directly it is available through Bio::SearchIO
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer2',
-file => 't/data/L77119.hmmer');
while( my $result = $in->next_result ) {
# this is a Bio::Search::Result::HMMERResult object
print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
while( my $hit = $result->next_hit ) {
print $hit->name(), "\n";
while( my $hsp = $hit->next_hsp ) {
print "length is ", $hsp->length(), "\n";
}
}
}
DESCRIPTION
This object implements a parser for HMMER output.
FEEDBACK
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
Support
Please direct usage questions or support issues to the mailing list:
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.
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::SearchIO::hmmer2->new();
Function: Builds a new Bio::SearchIO::hmmer2 object
Returns : Bio::SearchIO::hmmer2
Args : -fh/-file => HMMER filename
-format => 'hmmer2'
next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
start_element
Title : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
end_element
Title : start_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
element
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
within_element
Title : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
in_element
Title : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'within' because 'in' only
tests its immediete parent.
Returns : boolean
Args : string element name
start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
result_count
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
#
# BioPerl module for Bio::SearchIO::hmmer2
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
# Let the code begin...
package Bio::SearchIO::hmmer2;
use strict;
use Bio::Factory::ObjectFactory;
use vars qw(%MAPPING %MODEMAP
);
use base qw(Bio::SearchIO::hmmer);
BEGIN {
# mapping of HMMER items to Bioperl hash keys
%MODEMAP = (
'HMMER_Output' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
%MAPPING = (
'Hsp_bit-score' => 'HSP-bits',
'Hsp_score' => 'HSP-score',
'Hsp_evalue' => 'HSP-evalue',
'Hsp_query-from' => 'HSP-query_start',
'Hsp_query-to' => 'HSP-query_end',
'Hsp_hit-from' => 'HSP-hit_start',
'Hsp_hit-to' => 'HSP-hit_end',
'Hsp_positive' => 'HSP-conserved',
'Hsp_identity' => 'HSP-identical',
'Hsp_gaps' => 'HSP-hsp_gaps',
'Hsp_hitgaps' => 'HSP-hit_gaps',
'Hsp_querygaps' => 'HSP-query_gaps',
'Hsp_qseq' => 'HSP-query_seq',
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_midline' => 'HSP-homology_seq',
'Hsp_align-len' => 'HSP-hsp_length',
'Hsp_query-frame' => 'HSP-query_frame',
'Hsp_hit-frame' => 'HSP-hit_frame',
'Hit_id' => 'HIT-name',
'Hit_len' => 'HIT-length',
'Hit_accession' => 'HIT-accession',
'Hit_desc' => 'HIT-description',
'Hit_signif' => 'HIT-significance',
'Hit_score' => 'HIT-score',
'HMMER_program' => 'RESULT-algorithm_name',
'HMMER_version' => 'RESULT-algorithm_version',
'HMMER_query-def' => 'RESULT-query_name',
'HMMER_query-len' => 'RESULT-query_length',
'HMMER_query-acc' => 'RESULT-query_accession',
'HMMER_querydesc' => 'RESULT-query_description',
'HMMER_hmm' => 'RESULT-hmm_name',
'HMMER_seqfile' => 'RESULT-sequence_file',
'HMMER_db' => 'RESULT-database_name',
);
}
sub _initialize {
my ( $self, @args ) = @_;
$self->SUPER::_initialize(@args);
$self->{'_hmmidline'} = 'HMMER 2.2g (August 2001)';
}
sub next_result {
my ($self) = @_;
my $seentop = 0;
my $reporttype;
my ( $last, @hitinfo, @hspinfo, %hspinfo, %hitinfo );
local $/ = "\n";
local $_;
my $verbose = $self->verbose; # cache for speed?
$self->start_document();
local ($_);
while ( defined( $_ = $self->_readline ) ) {
my $lineorig = $_;
chomp;
if (/^HMMER\s+(\S+)\s+\((.+)\)/o) {
my ( $prog, $version ) = split;
if ($seentop) {
$self->_pushback($_);
$self->end_element( { 'Name' => 'HMMER_Output' } );
return $self->end_document();
}
$self->{'_hmmidline'} = $_;
$self->start_element( { 'Name' => 'HMMER_Output' } );
$self->{'_result_count'}++;
$seentop = 1;
if ( defined $last ) {
($reporttype) = split( /\s+/, $last );
$self->element(
{
'Name' => 'HMMER_program',
'Data' => uc($reporttype)
}
);
}
$self->element(
{
'Name' => 'HMMER_version',
'Data' => $version
}
);
}
elsif (s/^HMM file:\s+//o) {
$self->{'_hmmfileline'} = $lineorig;
$self->element(
{
'Name' => 'HMMER_hmm',
'Data' => $_
}
);
}
elsif (s/^Sequence\s+(file|database):\s+//o) {
$self->{'_hmmseqline'} = $lineorig;
if ( $1 eq 'database' ) {
$self->element(
{
'Name' => 'HMMER_db',
'Data' => $_
}
);
}
$self->element(
{
'Name' => 'HMMER_seqfile',
'Data' => $_
}
);
}
elsif (s/^Query(\s+(sequence|HMM))?(?:\s+\d+)?:\s+//o) {
if ( !$seentop ) {
# we're in a multi-query report
$self->_pushback( $self->{'_hmmidline'} );
$self->_pushback( $self->{'_hmmfileline'} );
$self->_pushback( $self->{'_hmmseqline'} );
$self->_pushback($lineorig);
next;
}
s/\s+$//;
$self->element(
{
'Name' => 'HMMER_query-def',
'Data' => $_
}
);
}
elsif (s/^Accession:\s+//o) {
s/\s+$//;
$self->element(
{
'Name' => 'HMMER_query-acc',
'Data' => $_
}
);
}
elsif (s/^Description:\s+//o) {
s/\s+$//;
$self->element(
{
'Name' => 'HMMER_querydesc',
'Data' => $_
}
);
}
elsif ( defined $self->{'_reporttype'}
&& $self->{'_reporttype'} eq 'HMMSEARCH' )
{
# PROCESS HMMSEARCH RESULTS HERE
if (/^Scores for complete sequences/o) {
while ( defined( $_ = $self->_readline ) ) {
last if (/^\s+$/);
next if ( /^Sequence\s+Description/o || /^\-\-\-/o );
my @line = split;
my ( $name, $n, $evalue, $score ) =
( shift @line, pop @line, pop @line, pop @line );
my $desc = join( ' ', @line );
push @hitinfo, [ $name, $desc, $evalue, $score ];
$hitinfo{$name} = $#hitinfo;
}
}
elsif (/^Parsed for domains:/o) {
@hspinfo = ();
while ( defined( $_ = $self->_readline ) ) {
last if (/^\s+$/);
if (m!^//!) {
$self->_pushback($_);
last;
}
next if ( /^(Model|Sequence)\s+Domain/ || /^\-\-\-/ );
chomp;
if (
my ( $n, $domainnum, $domainct, @vals ) = (
m!^(\S+)\s+ # host name
(\d+)/(\d+)\s+ # num/num (ie 1 of 2)
(\d+)\s+(\d+).+? # sequence start and end
(\d+)\s+(\d+)\s+ # hmm start and end
\S+\s+ # []
(\S+)\s+ # score
(\S+) # evalue
\s*$!ox
)
)
{
# array lookup so that we can get rid of things
# when they've been processed
my $info = $hitinfo[ $hitinfo{$n} ];
if ( !defined $info ) {
$self->warn(
"Incomplete Sequence information, can't find $n hitinfo says $hitinfo{$n}"
);
next;
}
push @hspinfo, [ $n, @vals ];
}
}
}
elsif (/^Alignments of top/o) {
my ( $prelength, $lastdomain, $count, $width );
$count = 0;
my %domaincounter;
my $second_tier = 0;
while ( defined( $_ = $self->_readline ) ) {
next if ( /^Align/o
|| /^\s+RF\s+[x\s]+$/o );
if ( /^Histogram/o || m!^//!o ) {
if ( $self->in_element('hsp') ) {
$self->end_element( { 'Name' => 'Hsp' } );
}
if ( $self->within_element('hit') ) {
$self->end_element( { 'Name' => 'Hit' } );
}
last;
}
chomp;
if (
m/^\s*(.+):\s+domain\s+(\d+)\s+of\s+(\d+)\,\s+
from\s+(\d+)\s+to\s+(\d+)/x
)
{
my ( $name, $domainct, $domaintotal, $from, $to ) =
( $1, $2, $3, $4, $5 );
$domaincounter{$name}++;
if ( $self->within_element('hit') ) {
if ( $self->within_element('hsp') ) {
$self->end_element( { 'Name' => 'Hsp' } );
}
$self->end_element( { 'Name' => 'Hit' } );
}
$self->start_element( { 'Name' => 'Hit' } );
my $info = [
@{
$hitinfo[ $hitinfo{$name} ] || $self->throw(
"Could not find hit info for $name: Insure that your database contains only unique sequence names"
)
}
];
if ( $info->[0] ne $name ) {
$self->throw(
"Somehow the Model table order does not match the order in the domains (got "
. $info->[0]
. ", expected $name)" );
}
$self->element(
{
'Name' => 'Hit_id',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_desc',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_signif',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_score',
'Data' => shift @{$info}
}
);
$self->start_element( { 'Name' => 'Hsp' } );
$self->element(
{
'Name' => 'Hsp_identity',
'Data' => 0
}
);
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => 0
}
);
my $HSPinfo = shift @hspinfo;
my $id = shift @$HSPinfo;
if ( $id ne $name ) {
$self->throw(
"Somehow the domain list details do not match the table (got $id, expected $name)"
);
}
if ( $domaincounter{$name} == $domaintotal ) {
$hitinfo[ $hitinfo{$name} ] = undef;
}
$self->element(
{
'Name' => 'Hsp_hit-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_hit-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_query-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_query-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_score',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => shift @$HSPinfo
}
);
$lastdomain = $name;
}
else {
# Might want to change this so that it
# accumulates all the of the alignment lines into
# three array slots and then tests for the
# end of the line
if (/^(\s+\*\-\>)(\S+)/o) { # start of domain
$prelength = CORE::length($1);
$width = 0;
# deal with fact that start en stop is on same line
my $data = $2;
if ($data =~ s/\<\-?\*?\s*$//)
{
$width = CORE::length($data);
}
$self->element(
{
'Name' => 'Hsp_qseq',
'Data' => $data
}
);
$count = 0;
$second_tier = 0;
}
elsif (/^(\s+)(\S+)\<\-\*\s*$/o) { #end of domain
$self->element(
{
'Name' => 'Hsp_qseq',
'Data' => $2
}
);
$width = CORE::length($2);
$count = 0;
}
elsif (( $count != 1 && /^\s+$/o )
|| CORE::length($_) == 0
|| /^\s+\-?\*\s*$/ )
{
next;
}
elsif ( $count == 0 ) {
$prelength -= 3 unless ( $second_tier++ );
unless ( defined $prelength ) {
# $self->warn("prelength not set");
next;
}
$self->element(
{
'Name' => 'Hsp_qseq',
'Data' => substr( $_, $prelength )
}
);
}
elsif ( $count == 1 ) {
if ( !defined $prelength ) {
$self->warn("prelength not set");
}
if ($width) {
$self->element(
{
'Name' => 'Hsp_midline',
'Data' =>
substr( $_, $prelength, $width )
}
);
}
else {
$self->element(
{
'Name' => 'Hsp_midline',
'Data' => substr( $_, $prelength )
}
);
}
}
elsif ( $count == 2 ) {
if (/^\s+(\S+)\s+(\d+|\-)\s+(\S*)\s+(\d+|\-)/o) {
$self->element(
{
'Name' => 'Hsp_hseq',
'Data' => $3
}
);
}
else {
$self->warn("unrecognized line: $_\n");
}
}
$count = 0 if $count++ >= 2;
}
}
}
elsif ( /^Histogram/o || m!^//!o ) {
while ( my $HSPinfo = shift @hspinfo ) {
my $id = shift @$HSPinfo;
my $info = [ @{ $hitinfo[ $hitinfo{$id} ] } ];
next unless defined $info;
$self->start_element( { 'Name' => 'Hit' } );
$self->element(
{
'Name' => 'Hit_id',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_desc',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_signif',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_score',
'Data' => shift @{$info}
}
);
$self->start_element( { 'Name' => 'Hsp' } );
$self->element(
{
'Name' => 'Hsp_query-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_query-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_hit-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_hit-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_score',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_identity',
'Data' => 0
}
);
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => 0
}
);
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => 0
}
);
$self->end_element( { 'Name' => 'Hsp' } );
$self->end_element( { 'Name' => 'Hit' } );
}
@hitinfo = ();
%hitinfo = ();
last;
}
}
elsif ( defined $self->{'_reporttype'}
&& $self->{'_reporttype'} eq 'HMMPFAM' )
{
# process HMMPFAM results here
if (/^Scores for sequence family/o) {
while ( defined( $_ = $self->_readline ) ) {
last if (/^\s+$/);
next if ( /^Model\s+Description/o || /^\-\-\-/o );
chomp;
my @line = split;
my ( $model, $n, $evalue, $score ) =
( shift @line, pop @line, pop @line, pop @line );
my $desc = join( ' ', @line );
push @hitinfo, [ $model, $desc, $score, $evalue, $n ];
$hitinfo{$model} = $#hitinfo;
}
}
elsif (/^Parsed for domains:/o) {
@hspinfo = ();
while ( defined( $_ = $self->_readline ) ) {
last if (/^\s+$/);
if (m!^//!) {
$self->_pushback($_);
last;
}
next if ( /^Model\s+Domain/o || /^\-\-\-/o );
chomp;
if (
my ( $n, $domainnum, $domainct, @vals ) = (
m!^(\S+)\s+ # domain name
(\d+)/(\d+)\s+ # domain num out of num
(\d+)\s+(\d+).+? # seq start, end
(\d+)\s+(\d+)\s+ # hmm start, end
\S+\s+ # []
(\S+)\s+ # score
(\S+) # evalue
\s*$!ox
)
)
{
my $hindex = $hitinfo{$n};
if ( !defined $hindex ) {
push @hitinfo,
[ $n, '', $vals[5], $vals[6], $domainct ];
$hitinfo{$n} = $#hitinfo;
$hindex = $#hitinfo;
}
my $info = $hitinfo[$hindex];
if ( !defined $info ) {
$self->warn(
"incomplete Domain information, can't find $n hitinfo says $hitinfo{$n}"
);
next;
}
push @hspinfo, [ $n, @vals ];
}
}
}
elsif (/^Alignments of top/o) {
my ( $prelength, $lastdomain, $count, $width );
$count = 0;
my $second_tier = 0;
while ( defined( $_ = $self->_readline ) ) {
next
if (
/^Align/o
|| ( $count != 1
&& /^\s+RF\s+[x\s]+$/o )
);
# fix for bug 2632
next if ($_ =~ m/^\s+CS\s+/o && $count == 0);
if ( /^Histogram/o || m!^//!o || /^Query sequence/o ) {
if ( $self->in_element('hsp') ) {
$self->end_element( { 'Name' => 'Hsp' } );
}
if ( $self->in_element('hit') ) {
$self->end_element( { 'Name' => 'Hit' } );
}
$self->_pushback($_);
last;
}
chomp;
if (m/(\S+):.*from\s+(\d+)\s+to\s+(\d+)/o) {
my ( $name, $from, $to ) = ( $1, $2, $3 );
if ( $self->within_element('hit') ) {
if ( $self->in_element('hsp') ) {
$self->end_element( { 'Name' => 'Hsp' } );
}
$self->end_element( { 'Name' => 'Hit' } );
}
my $info = [ @{ $hitinfo[ $hitinfo{$name} ] } ];
if ( !defined $info
|| $info->[0] ne $name )
{
$self->warn(
"Somehow the Model table order does not match the order in the domains (got "
. $info->[0]
. ", expected $name). We're back loading this from the alignment information instead"
);
$info = [
$name, '',
/score\s+([^,\s]+),\s+E\s+=\s+(\S+)/ox
];
push @hitinfo, $info;
$hitinfo{$name} = $#hitinfo;
}
$self->start_element( { 'Name' => 'Hit' } );
$self->element(
{
'Name' => 'Hit_id',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_desc',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_score',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_signif',
'Data' => shift @{$info}
}
);
$self->start_element( { 'Name' => 'Hsp' } );
$self->element(
{
'Name' => 'Hsp_identity',
'Data' => 0
}
);
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => 0
}
);
my $HSPinfo = shift @hspinfo;
my $id = shift @$HSPinfo;
if ( $id ne $name ) {
$self->throw(
"Somehow the domain list details do not match the table (got $id, expected $name)"
);
}
$self->element(
{
'Name' => 'Hsp_query-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_query-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_hit-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_hit-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_score',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => shift @$HSPinfo
}
);
$lastdomain = $name;
}
else {
if (/^(\s+\*\-\>)(\S+)/o) {
# start of domain
$prelength = CORE::length($1);
$width = 0;
# deal with fact that start en stop is on same line
my $data = $2;
if ($data =~ s/\<\-?\*?\s*$//)
{
$width = CORE::length($data);
}
$self->element(
{
'Name' => 'Hsp_hseq',
'Data' => $data
}
);
$count = 0;
$second_tier = 0;
}
elsif (/^(\s+)(\S+)\<\-?\*?\s*$/o) {
#end of domain
$prelength -= 3 unless ( $second_tier++ );
$self->element(
{
'Name' => 'Hsp_hseq',
'Data' => $2
}
);
$width = CORE::length($2);
$count = 0;
}
elsif (CORE::length($_) == 0
|| ( $count != 1 && /^\s+$/o )
|| /^\s+\-?\*\s*$/ )
{
next;
}
elsif ( $count == 0 ) {
$prelength -= 3 unless ( $second_tier++ );
unless ( defined $prelength ) {
# $self->warn("prelength not set");
next;
}
$self->element(
{
'Name' => 'Hsp_hseq',
'Data' => substr( $_, $prelength )
}
);
}
elsif ( $count == 1 ) {
if ( !defined $prelength ) {
$self->warn("prelength not set");
}
if ($width) {
$self->element(
{
'Name' => 'Hsp_midline',
'Data' =>
substr( $_, $prelength, $width )
}
);
}
else {
$self->element(
{
'Name' => 'Hsp_midline',
'Data' => substr( $_, $prelength )
}
);
}
}
elsif ( $count == 2 ) {
if ( /^\s+(\S+)\s+(\d+)\s+(\S+)\s+(\d+)/o
|| /^\s+(\S+)\s+(\-)\s+(\S*)\s+(\-)/o )
{
$self->element(
{
'Name' => 'Hsp_qseq',
'Data' => $3
}
);
}
else {
$self->throw(
"unrecognized line ($count): $_\n");
}
}
$count = 0 if $count++ >= 2;
}
}
}
elsif ( /^Histogram/o || m!^//!o ) {
while ( my $HSPinfo = shift @hspinfo ) {
my $id = shift @$HSPinfo;
my $info = [ @{ $hitinfo[ $hitinfo{$id} ] } ];
next unless defined $info;
$self->start_element( { 'Name' => 'Hit' } );
$self->element(
{
'Name' => 'Hit_id',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_desc',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_signif',
'Data' => shift @{$info}
}
);
$self->element(
{
'Name' => 'Hit_score',
'Data' => shift @{$info}
}
);
$self->start_element( { 'Name' => 'Hsp' } );
$self->element(
{
'Name' => 'Hsp_query-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_query-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_hit-from',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_hit-to',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_score',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => shift @$HSPinfo
}
);
$self->element(
{
'Name' => 'Hsp_identity',
'Data' => 0
}
);
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => 0
}
);
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => 0
}
);
$self->end_element( { 'Name' => 'Hsp' } );
$self->end_element( { 'Name' => 'Hit' } );
}
@hitinfo = ();
%hitinfo = ();
last;
}
# uncomment to see missed lines with verbose on
#else {
# $self->debug($_);
#}
}
$last = $_;
}
$self->end_element( { 'Name' => 'HMMER_Output' } ) unless !$seentop;
return $self->end_document();
}
sub start_element {
my ( $self, $data ) = @_;
# we currently don't care about attributes
my $nm = $data->{'Name'};
my $type = $MODEMAP{$nm};
if ($type) {
if ( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf( "start_%s", lc $type );
$self->_eventHandler->$func( $data->{'Attributes'} );
}
unshift @{ $self->{'_elements'} }, $type;
}
if ( defined $type
&& $type eq 'result' )
{
$self->{'_values'} = {};
$self->{'_result'} = undef;
}
}
sub end_element {
my ( $self, $data ) = @_;
my $nm = $data->{'Name'};
my $type = $MODEMAP{$nm};
my $rc;
if ( $nm eq 'HMMER_program' ) {
if ( $self->{'_last_data'} =~ /(HMM\S+)/i ) {
$self->{'_reporttype'} = uc $1;
}
}
# Hsp are sort of weird, in that they end when another
# object begins so have to detect this in end_element for now
if ( $nm eq 'Hsp' ) {
foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq)) {
my $data = $self->{'_last_hspdata'}->{$_};
if ($data && $_ eq 'Hsp_hseq') {
# replace hmm '.' gap symbol by '-'
$data =~ s/\./-/g;
}
$self->element(
{
'Name' => $_,
'Data' => $data
}
);
}
$self->{'_last_hspdata'} = {};
}
if ($type) {
if ( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf( "end_%s", lc $type );
$rc = $self->_eventHandler->$func( $self->{'_reporttype'},
$self->{'_values'} );
}
my $lastelem = shift @{ $self->{'_elements'} };
}
elsif ( $MAPPING{$nm} ) {
if ( ref( $MAPPING{$nm} ) =~ /hash/i ) {
my $key = ( keys %{ $MAPPING{$nm} } )[0];
$self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } =
$self->{'_last_data'};
}
else {
$self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'};
}
}
else {
$self->debug("unknown nm $nm, ignoring\n");
}
$self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if ( defined $type && $type eq 'result' );
return $rc;
}
sub element {
my ( $self, $data ) = @_;
$self->start_element($data);
$self->characters($data);
$self->end_element($data);
}
sub characters {
my ( $self, $data ) = @_;
if ( $self->in_element('hsp')
&& $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/o
&& defined $data->{'Data'} )
{
$self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'};
}
return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o );
$self->{'_last_data'} = $data->{'Data'};
}
sub within_element {
my ( $self, $name ) = @_;
return 0
if ( !defined $name
|| !defined $self->{'_elements'}
|| scalar @{ $self->{'_elements'} } == 0 );
foreach ( @{ $self->{'_elements'} } ) {
return 1 if ( $_ eq $name );
}
return 0;
}
sub in_element {
my ( $self, $name ) = @_;
return 0 if !defined $self->{'_elements'}->[0];
return ( $self->{'_elements'}->[0] eq $name );
}
sub start_document {
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'} = undef;
$self->{'_elements'} = [];
}
sub end_document {
my ($self) = @_;
return $self->{'_result'};
}
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
1;