# $Id: bioperl.lisp 15559 2009-02-23 12:11:20Z maj $
#
# BioPerl module for Bio::SearchIO::hmmer3
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Thomas Sharpton <thomas.sharpton@gmail.com>
#
# Copyright Thomas Sharpton
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO::hmmer3 - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=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:
L<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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Thomas Sharpton
Email thomas.sharpton@gmail.com
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=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::SearchIO::hmmer3;
use strict;
use Data::Dumper;
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',
);
}
=head2 new
Title : new
Usage : my $obj = new Bio::SearchIO::Hmmer3->new();
Function: Builds a new Bio::SearchIO::Hmmer3 object
Returns : an instance of Bio::SearchIO::Hmmer3
Args : -fh/-file => HMMER filename
-format => 'hmmer3'
=cut
sub _initialize {
my( $self,@args ) = @_;
$self->SUPER::_initialize(@args);
$self->{'_hmmidline'} = 'HMMER 3.0b placeholder';
$self->{'_alnreport'} = 1; #does report include alignments
}
=head2 next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub next_result{
my ($self) = @_;
my $seentop = 0; #Placeholder for when we deal with multi-query reports
my $reporttype;
my ( $last, @hit_list, @hsp_list, %hspinfo, %hitinfo, %domaincounter );
local $/ = "\n";
local $_;
my $verbose = $self->verbose; # cache for speed? JES's idea in hmmer.pm
$self->start_document();
local ($_);
#This is here to ensure that next_result doesn't produce infinite loop
if(!defined( $_ = $self->_readline) ) {
return undef;
}
else{
$self->_pushback($_);
}
#Regex goes here for HMMER3
#Start with hmmsearch processing
while ( defined( $_ = $self->_readline ) ) {
my $lineorig = $_;
chomp;
#Grab the program name.
if ( $_ =~ m/^\#\s(\S+)\s\:\:\s/ ){
my $prog = $1;
#TO DO LATER: customize the above regex to adapt to other
#program types!!! (hmmscan, etc)
$self->start_element( { 'Name' => 'HMMER_Output' } );
$self->{'_result_count'}++; #Might need to move to another block
$self->element(
{
'Name' => 'HMMER_program',
'Data' => uc($prog)
}
);
}
#Get the HMMER package version and release date
elsif ( $_ =~ m/^\#\sHMMER\s+(\S+)\s+\((.+)\)/ ) {
my $version = $1;
my $versiondate = $2;
$self->{'_hmmidline'} = $_;
$self->element(
{
'Name' => 'HMMER_version',
'Data' => $version
}
);
}
#Get the query info
elsif( $_ =~ /^\#\squery \w+ file\:\s+(\S+)/ ){
if( $self->{'_reporttype'} eq 'HMMSEARCH') {
$self->{'_hmmfileline'} = $lineorig;
$self->element(
{
'Name' => 'HMMER_hmm',
'Data' => $1
}
);
}
elsif( $self->{'_reporttype'} eq 'HMMSCAN' ) {
$self->{'_hmmseqline'} = $lineorig;
$self->element(
{
'Name' => 'HMMER_seqfile',
'Data' => $1
}
);
}
}
#If this is a report without alignments
elsif( $_ =~ m/^\#\sshow\salignments\sin\soutput/ ){
$self->{'_alnreport'} = 0;
}
#Get the database info
elsif( $_ =~ m/^\#\starget\s\S+\sdatabase\:\s+(\S+)/ ){
# $self->{'_hmmseqline'} = $lineorig;
# $self->element(
# {
# 'Name' => 'HMMER_seqfile',
# 'Data' => $1
# }
# );
if( $self->{'_reporttype'} eq 'HMMSEARCH') {
$self->{'_hmmseqline'} = $lineorig;
$self->element(
{
'Name' => 'HMMER_seqfile',
'Data' => $1
}
);
}
elsif( $self->{'_reporttype'} eq 'HMMSCAN' ) {
$self->{'_hmmfileline'} = $lineorig;
$self->element(
{
'Name' => 'HMMER_hmm',
'Data' => $1
}
);
}
}
#Get query data
elsif( $_ =~ s/^Query:\s+// ) {
#TODO Code to deal with multi query report
unless( s/\s+\[[L|M]\=(\d+)\]$// ){
warn "Error parsing length for query, offending line $_\n";
exit(0);
}
my $querylen = $1;
$self->element(
{
'Name' => 'HMMER_query-len',
'Data' => $querylen
}
);
$self->element(
{
'Name' => 'HMMER_query-def',
'Data' => $_
}
);
}
#Get Accession data
elsif( $_ =~ s/^Accession:\s+// ){
s/\s+$//;
$self->element(
{
'Name' => 'HMMER_query-acc',
'Data' => $_
}
);
}
#Get description data
elsif( $_ =~ s/^Description:\s+// ){
s/\s+$//;
$self->element(
{
'Name' => 'HMMER_querydesc',
'Data' => $_
}
);
}
#PROCESS HMMSEARCH AND HMMSCAN RESULTS SPECIFIC FORMATTING HERE
elsif( defined $self->{'_reporttype'} &&
(
$self->{'_reporttype'} eq 'HMMSEARCH' ||
$self->{'_reporttype'} eq 'HMMSCAN'
)
){
#Complete sequence table data above inclusion threshold
if( $_ =~ m/Scores for complete sequence/){
while (defined( $_ = $self->_readline ) ) {
if ($_ =~ m/inclusion threshold/ || m/Domain( and alignment)? annotation for each/ ||
m/\[No hits detected/ || m!^//! ){
$self->_pushback($_);
last;
}
#grab table data
next if ( m/\-\-\-/ || m/^\s+E\-value\s+score/ || m/^$/);
my (
$eval_full, $score_full, $bias_full,
$eval_best, $score_best, $bias_best,
$exp, $n, $hitid, $desc, @hitline
);
@hitline = split(" ", $_);
$eval_full = shift @hitline;
$score_full = shift @hitline;
$bias_full = shift @hitline;
$eval_best = shift @hitline;
$score_best = shift @hitline;
$bias_best = shift @hitline;
$exp = shift @hitline;
$n = shift @hitline;
$hitid = shift @hitline;
$desc = join " ", @hitline;
if( !defined( $desc ) ){
$desc = "";
}
push @hit_list, [ $hitid, $desc, $eval_full, $score_full ];
$hitinfo{$hitid}= $#hit_list;
}
}
#Complete sequence table data below inclusion threshold
#not currently fully implemented
elsif( $_ =~ m/inclusion threshold/ ){
while( defined( $_ = $self->_readline ) ) {
if( $_ =~ m/Domain( and alignment)? annotation for each/ ||
m/Internal pipeline statistics summary/ ){
$self->_pushback($_);
last;
}
next if( $_ =~ m/^$/ );
my (
$eval_full, $score_full, $bias_full,
$eval_best, $score_best, $bias_best,
$exp, $n, $hitid, $desc, @hitline
);
@hitline = split(" ", $_);
$eval_full = shift @hitline;
$score_full = shift @hitline;
$bias_full = shift @hitline;
$eval_best = shift @hitline;
$score_best = shift @hitline;
$bias_best = shift @hitline;
$exp = shift @hitline;
$n = shift @hitline;
$hitid = shift @hitline;
$desc = join " ", @hitline;
$hitinfo{$hitid} = "below_inclusion";
}
}
#Domain annotation for each sequence table data
elsif( $_ =~ m/Domain( and alignment)? annotation for each/){
@hsp_list = (); #here for multi-query reports
my $name;
while( defined( $_ = $self->_readline ) ) {
if ($_ =~ m/Internal pipeline statistics/ || m/\[No targets detected/ ){
$self->_pushback($_);
last;
}
if( $_ =~ m/^\>\>\s(.*?)\s+/ ) {
$name = $1;
#skip hits below inclusion threshold
next if( $hitinfo{$name} eq "below_inclusion");
$domaincounter{$name} = 0;
while( defined( $_ = $self->_readline ) ) {
#grab table data for sequence
if ($_ =~ m/Internal pipeline statistics/ ||
$_ =~ m/^\>\>/ ){
$self->_pushback($_);
last;
}
if ( $_ =~ m/Alignments for each domain/ ) {
$self->_pushback($_);
last;
}
if ( $_ =~ m/^\s+\#\s+score/ ||
$_ =~ m/^\s\-\-\-\s+/ ||
# $_ =~ m/^\>\>/ ||
$_ =~ m/^$/ ){
next;
}
# grab hsp data from table, push into @hsp;
if(
my ($domain_num, $score, $bias, $ceval,
$ieval, $hmmstart, $hmmstop,
$qalistart, $qalistop, $envstart,
$envstop, $envbound, $acc) =
m!^\s+(\d+)\s\!*\?*\s+ #domain num
(\S+)\s+(\S+)\s+ #score, bias
(\S+)\s+(\S+)\s+ #c-eval, i-eval
(\d+)\s+(\d+).+? #hmm start, stop
(\d+)\s+(\d+).+? #query start, stop
(\d+)\s+(\d+).+? #env start, stop
(\S+) #acc
\s*$!ox
){
#keeping simple for now. let's customize later
my @vals = ($hmmstart, $hmmstop, $qalistart, $qalistop, $score, $ceval, '', '', '');
my $info = $hit_list[ $hitinfo{$name} ];
if( !defined $info ){
$self->warn(
"Incomplete sequence information; can't find $name, hitinfo says $hitinfo{$name}\n"
);
next;
}
$domaincounter{$name}++;
my $hsp_key = $name . "_" . $domaincounter{$name};
push @hsp_list, [ $name, @vals ];
$hspinfo{$hsp_key} = $#hsp_list;
}
else{
print "missed this line: $_\n";
}
}
}
elsif ($_ =~ m/Alignments for each domain/ ) {
my $domain_count = 0;
#line counter
my $count = 0;
# There's an optional block, so we sometimes need to
# count to 3, and sometimes to 4.
my $max_count = 3;
my $lastdomain;
my $hsp;
my ($hline, $midline, $qline);
while( defined( $_ = $self->_readline ) ) {
if( $_ =~ m/^\>\>/ ||
$_ =~ m/Internal pipeline statistics/){
$self->_pushback($_);
last;
}
elsif( $hitinfo{$name} eq "below_inclusion" ||
$_ =~ m/^$/ ) {
next;
}
elsif( $_ =~ /\s\s\=\=\sdomain\s(\d+)\s+/){
my $domainnum = $1;
$count = 0;
my $key = $name . "_" . $domainnum;
$hsp = $hsp_list[ $hspinfo{$key} ];
$hline = $$hsp[-3];
$midline = $$hsp[-2];
$qline = $$hsp[-1];
$lastdomain = $name;
}
# model data track, some reports don't have
elsif( $_ =~ m/\s+\S+\sCS$/ ){
my $modeltrack = $_;
$max_count++;
$count++;
next;
}
elsif( $count == $max_count - 3 ){
#hit sequence
my @data = split(" ", $_);
my $seq = $data[-2];
$hline .= $seq;
$count++;
next;
}
elsif( $count == $max_count - 2 ){
#conservation track
#storage isn't quite right - need to remove
#leading/lagging whitespace while preserving
#gap data (latter isn't done, former is)
$_ =~ s/^\s+//;
$_ =~ s/\s+$//;
$midline .= $_;
$count++;
next;
}
elsif( $count == $max_count - 1 ){
#query track
my @data = split(" ", $_);
my $seq = $data[-2];
$qline .= $seq;
$count++;
next;
}
elsif( $count == $max_count ){
#pval track
my $pvals = $_;
$count = 0;
$max_count = 3;
$$hsp[-3] = $hline;
$$hsp[-2] = $midline;
$$hsp[-1] = $qline;
next;
}
else{
print "missed $_\n";
}
}
}
}
}
elsif( m/Internal pipeline statistics/ || m!^//! ){
# if within hit, hsp close;
if ( $self->within_element('hit') ) {
if ( $self->within_element('hsp') ) {
$self->end_element( { 'Name' => 'Hsp' } );
}
$self->end_element( { 'Name' => 'Hit' } );
}
#grab summary statistics of run
while( defined( $_ = $self->_readline ) ) {
last if ( $_ =~ m/^\/\/$/ );
}
#Jason does a lot of processing of hits/hsps here;
while( my $hit = shift @hit_list ) {
my $hit_name = shift @$hit;
my $hit_desc = shift @$hit;
my $hit_signif = shift @$hit;
my $hit_score = shift @$hit;
my $num_domains = $domaincounter{$hit_name} || 0;
$self->start_element( { 'Name' => 'Hit' } );
$self->element(
{
'Name' => 'Hit_id',
'Data' => $hit_name
}
);
$self->element(
{
'Name' => 'Hit_desc',
'Data' => $hit_desc
}
);
$self->element(
{
'Name' => 'Hit_signif',
'Data' => $hit_signif
}
);
$self->element(
{
'Name' => 'Hit_score',
'Data' => $hit_score
}
);
for my $i (1..$num_domains) {
my $key = $hit_name . "_" . $i;
my $hsp = $hsp_list[ $hspinfo{$key} ];
if(defined $hsp) {
my $hsp_name = shift @$hsp;
$self->start_element( { 'Name' => 'Hsp' } );
$self->element( {
'Name' => 'Hsp_identity',
'Data' => 0
} );
$self->element( {
'Name' => 'Hsp_positive',
'Data' => 0
} );
$self->element( {
'Name' => 'Hsp_hit-from',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_hit-to',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_query-from',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_query-to',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_score',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_evalue',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_hseq',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_midline',
'Data' => shift @$hsp
} );
$self->element( {
'Name' => 'Hsp_qseq',
'Data' => shift @$hsp
} );
$self->end_element( { 'Name' => 'Hsp' } );
}
}
$self->end_element( { 'Name' => 'Hit' } );
}
@hit_list = ();
%hitinfo = ();
last;
}
}
else{
print "missed: $_\n";
$self->debug($_);
}
$last = $_;
}
$self->end_element( { 'Name' => 'HMMER_Output' } );
my $result = $self->end_document();
return $result;
}
=head2 start_element
Title : start_element
Usage : $eventgenerator->start_element
Function: Handles a start event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
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;
}
}
=head2 end_element
Title : end_element
Usage : $eventgeneartor->end_element
Function: Handles and end element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
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'};
# print "lastdata is " . $self->{'_last_data'} . "\n";
}
}
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;
}
=head2 element
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convienence method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
=cut
sub element{
my ( $self, $data ) = @_;
$self->start_element($data);
$self->characters($data);
$self->end_element($data);
}
=head2 characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
=cut
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'};
}
=head2 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
=cut
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;
}
=head2 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 immediate parent
Returns : boolean
Args : string element name
=cut
sub in_element{
my ( $self, $name ) = @_;
return 0 if !defined $self->{'_elements'}->[0];
return ( $self->{'_elements'}->[0] eq $name );
}
=head2 start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
=cut
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'} = undef;
$self->{'_elements'} = [];
}
=head2 end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub end_document{
my ($self) = @_;
return $self->{'_result'};
}
=head2 result_count
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results processed
Returns : interger
Args : none
=cut
sub result_count{
my $self = shift;
return $self->{'_result_count'};
}
1;