#
# BioPerl module for Bio::SearchIO::rnamotif
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields <cjfields-at-uiuc-dot-edu>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser
=head1 SYNOPSIS
# do not call this module directly. Use Bio::SearchIO.
=head1 DESCRIPTION
This is a highly experimental SearchIO-based parser for output from the rnamotif
program (one of the programs in the RNAMotif suite). It currently parses only
raw rnamotif output for RNAMotif versions 3.0 and above; older versions may work
but will not be supported. rmfmt output will not be supported at this time.
=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:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Chris Fields
Email cjfields-at-uiuc-dot-edu
=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::rnamotif;
use strict;
use base qw(Bio::SearchIO);
my %MODEMAP = (
'Result' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
my %MAPPING = (
# commented out tags have not been assigned
'Hsp_score' => 'HSP-score',
'Hsp_custom-data' => 'HSP-custom_score',
# rnamotif has no evalue
# descriptor has no start, end; same as hit start, end
'Hsp_query-from' => 'HSP-query_start',
'Hsp_query-to' => 'HSP-query_end',
'Hsp_hit-from' => 'HSP-hit_start',
'Hsp_hit-to' => 'HSP-hit_end',
# descriptor has no start, end
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_align-len' => 'HSP-hsp_length',
# build this from scratch, simple WUSS-format
'Hsp_structure' => 'HSP-meta',
'Hsp_stranded' => 'HSP-stranded',
# not supported for RNAMotif
'Hit_id' => 'HIT-name',
'Hit_accession' => 'HIT-accession',
'Hit_gi' => 'HIT-ncbi_gi',
'Hit_def' => 'HIT-description',
'Hit_score' => 'HIT-score', # best HSP score
'RNAMotif_program' => 'RESULT-algorithm_name', # get/set
'RNAMotif_version' => 'RESULT-algorithm_version', # get/set
'RNAMotif_query-def'=> 'RESULT-query_name', # get/set
# No length (query is a descriptor)
'RNAMotif_query-acc'=> 'RESULT-query_accession', # get/set
'RNAMotif_querydesc'=> 'RESULT-query_description', # get/set
'RNAMotif_db' => 'RESULT-database_name', # get/set
);
# use structure_delimiters to set custom delimiters
my @VALID_SYMBOLS = qw(5-prime 3-prime single-strand unknown);
my %STRUCTURE_SYMBOLS = (
'5-prime' => '<',
'3-prime' => '>',
'single-strand' => '.',
'unknown' => '?'
# may add more for quartets, triplets
);
my $DEFAULT_VERSION = '3.0.3';
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO->new();
Function: Builds a new Bio::SearchIO::rnamotif object
Returns : Bio::SearchIO::rnamotif parser
Args : -fh/-file => RNAMotif filename
-format => 'rnamotif'
-model => query model (or descriptor, in this case)
-database => database name (default undef)
-query_acc => query accession (default undef)
-hsp_minscore => minimum HSP score cutoff
-hsp_maxscore => maximum HSP score cutoff
-symbols => hash ref of structure symbols to use
(default symbols in %STRUCTURE_SYMBOLS hash)
=cut
sub _initialize {
my ( $self, @args ) = @_;
$self->SUPER::_initialize(@args);
my ($version, $model, $database, $maxcutoff, $mincutoff, $seqdistance,
$accession, $symbols) =
$self->_rearrange([qw(VERSION MODEL DATABASE HSP_MAXSCORE
HSP_MINSCORE SEQ_DISTANCE QUERY_ACC SYMBOLS)],@args);
my $handler = $self->_eventHandler;
$handler->register_factory(
'result',
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::Result::GenericResult',
-interface => 'Bio::Search::Result::ResultI',
-verbose => $self->verbose
)
);
$handler->register_factory(
'hit',
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::Hit::ModelHit',
-interface => 'Bio::Search::Hit::HitI',
-verbose => $self->verbose
)
);
$handler->register_factory(
'hsp',
Bio::Factory::ObjectFactory->new(
-type => 'Bio::Search::HSP::ModelHSP',
-interface => 'Bio::Search::HSP::HSPI',
-verbose => $self->verbose
)
);
$model && $self->model($model);
$database && $self->database($database);
$accession && $self->query_accession($accession);
$version ||= $DEFAULT_VERSION;
$self->algorithm_version($version);
$self->throw("Cannot define both a minimal and maximal cutoff")
if (defined($mincutoff) && defined($maxcutoff));
defined($mincutoff) && $self->hsp_minscore($mincutoff);
defined($maxcutoff) && $self->hsp_maxscore($maxcutoff);
$symbols ||= \%STRUCTURE_SYMBOLS;
$self->structure_symbols($symbols);
}
=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;
local $/ = "\n";
local $_;
my ($rm, $d, $descriptor, $file, $oktobuild);
my ($hitid, $hitdesc, $hspid, $lastid, $lastscore);
my $sprintf;
# user-determined Result data
my ($accession, $db, $model) =
($self->query_accession, $self->database, $self->model);
# HSP building options
my $hsp_min = $self->hsp_minscore;
my $hsp_max = $self->hsp_maxscore;
my $version = $self->algorithm_version;
my $laststart;
my $verbose = $self->verbose; # cache for speed?
$self->start_document();
PARSER:
while ( defined( my $line = $self->_readline ) ) {
# start of report
next if $line =~ m{^\s+$};
if (index($line,'#RM') == 0) {
if (index($line,'#RM scored') == 0 ) {
if ($seentop) {
$self->_pushback($line);
last PARSER;
}
$self->start_element({'Name' => 'Result'});
$self->element_hash({
'RNAMotif_program' => 'rnamotif',
'RNAMotif_version' => $version,
'RNAMotif_query-acc' => $accession,
'RNAMotif_db' => $db
});
$seentop = 1;
#$self->debug("Start result\n");
} elsif (index($line,'#RM descr') == 0) {
($rm, $d, $descriptor) = split ' ', $line, 3;
# toss $rm, $d; keep $descr
chomp $descriptor;
$self->{'_descriptor'} = $descriptor;
$self->element(
{'Name' => 'RNAMotif_querydesc',
'Data' => $descriptor}
);
} elsif(index($line,'#RM dfile') == 0) {
($rm, $d, $file) = split ' ', $line, 3;
# toss $rm, $d; keep $file
chomp $file;
$self->element(
{'Name' => 'RNAMotif_query-def',
'Data' => $file}
);
} else {
$self->debug("Unrecognized line: $line");
}
} elsif ($line =~ s{^>}{}) {
chomp $line;
($hitid, $hitdesc) = split ' ',$line,2;
if ($self->within_element('hit') && ($hitid ne $lastid)) {
$self->element(
{'Name' => 'Hit_score',
'Data' => $lastscore}
) if $lastscore;
$self->end_element({'Name' => 'Hit'});
$self->start_element({'Name' => 'Hit'});
} elsif (!$self->within_element('hit')) {
$self->start_element({'Name' => 'Hit'});
}
my ($gi, $acc, $ver) = $self->_get_seq_identifiers($hitid);
$self->element_hash({
'Hit_id' => $hitid,
'Hit_gi' => $gi,
'Hit_accession' => $ver ? "$acc.$ver" :
$acc ? $acc : $hitid,
'Hit_def' => $hitdesc}
);
$lastid = $hitid;
} elsif ($line =~ m{^(\S+)\s+(.+?)\s+(\d+)\s+(\d+)\s+(\d+)\s(.*)$}xm) {
chomp $line;
my $hspid = $1;
my ($score, $strand, $start, $length , $seq) = ($2, $3, $4, $5, $6);
$score *= 1; # implicitly cast any odd '0.000' to float
# sanity check ids
unless ($hitid eq $hspid) {
$self->throw("IDs do not match!");
}
# check score for possible sprintf data, mark as such, cache result
if (!defined($sprintf)) {
if ($score =~ m{[^0-9.-]+}gxms) {
if (defined $hsp_min || defined $hsp_max ) {
$self->warn("HSP data likely contains custom score; ".
"ignoring min/maxscore");
}
$sprintf = $oktobuild = 1;
} else {
$sprintf = 0;
}
}
if (!$sprintf) {
if (($hsp_min && $score <= $hsp_min)
|| ($hsp_max && ($score >= $hsp_max)) ) {
# do not build HSP
$oktobuild = 0;
} else {
$oktobuild = 1;
# store best hit score based on the hsp min/maxscore only
if (defined $hsp_min && $score > $hsp_min) {
$lastscore = $score if !$lastscore || $score > $lastscore;
} elsif (defined $hsp_max && $score < $hsp_max) {
$lastscore = $score if !$lastscore || $score < $lastscore;
}
}
}
# build HSP
if ($oktobuild) {
my $end;
# calculate start/end
if( $strand==0 ) {
$end = $start + $length -1;
} else {
$end = $start - $length + 1;
}
my ($rna, $meta) = $self->_motif2meta($seq, $descriptor);
$self->start_element({'Name' => 'Hsp'});
my $rnalen = $rna =~ tr{ATGCatgc}{ATGCatgc};
$self->element_hash({
'Hsp_stranded' => 'HIT',
'Hsp_hseq' => $rna,
'Hsp_query-from' => 1,
'Hsp_query-to' =>length($rna),
'Hsp_hit-from' => $start,
'Hsp_hit-to' => $end,
'Hsp_structure' => $meta,
'Hsp_align-len' => length($rna),
'Hsp_score' => $sprintf ? undef : $score,
'Hsp_custom-data' => $sprintf ? $score : undef,
});
$self->end_element({'Name' => 'Hsp'});
$oktobuild = 0 if (!$sprintf);
}
}
}
if ($self->within_element('hit')) {
$self->element(
{'Name' => 'Hit_score',
'Data' => $lastscore}
) if $lastscore;
$self->end_element( { 'Name' => 'Hit' } );
}
if ($seentop) {
$self->end_element( { 'Name' => 'Result' } );
}
return $self->end_document();
}
=head2 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'
=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 : start_element
Usage : $eventgenerator->end_element
Function: Handles an 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 $rc;
if ($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;
}
=head2 element
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convenience 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 ) = @_;
# simple data calls (%MAPPING) do not need start_element
$self->characters($data);
$self->end_element($data);
}
=head2 element_hash
Title : element
Usage : $eventhandler->element_hash({'Hsp_hit-from' => $start,
'Hsp_hit-to' => $end,
'Hsp_score' => $lastscore});
Function: Convenience method that takes multiple simple data elements and
maps to appropriate parameters
Returns : none
Args : Hash ref with the mapped key (in %MAPPING) and value
=cut
sub element_hash {
my ($self, $data) = @_;
$self->throw("Must provide data hash ref") if !$data || !ref($data);
for my $nm (sort keys %{$data}) {
next if $data->{$nm} && $data->{$nm} =~ m{^\s*$}o;
if ( $MAPPING{$nm} ) {
if ( ref( $MAPPING{$nm} ) =~ /hash/i ) {
my $key = ( keys %{ $MAPPING{$nm} } )[0];
$self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } =
$data->{$nm};
}
else {
$self->{'_values'}->{ $MAPPING{$nm} } = $data->{$nm};
}
}
}
}
=head2 characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
=cut
sub characters {
my ( $self, $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 we have processed
Returns : integer
Args : none
=cut
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
=head2 descriptor
Title : descriptor
Usage : my $descr = $parser->descriptor();
Function: Get/Set descriptor name. Some versions of RNAMotif do not add the
descriptor name to the output. This also overrides any name found
while parsing.
Returns : String (name of model)
Args : [optional] String (name of model)
=cut
sub descriptor {
my $self = shift;
return $self->{'_descriptor'} = shift if @_;
return $self->{'_descriptor'};
}
=head2 model
Title : model
Usage : my $model = $parser->model();
Function: Get/Set model; Infernal currently does not output
the model name (Rfam ID)
Returns : String (name of model)
Args : [optional] String (name of model)
Note : this is a synonym for descriptor()
=cut
sub model { shift->descriptor(@_) }
=head2 database
Title : database
Usage : my $database = $parser->database();
Function: Get/Set database; Infernal currently does not output
the database name
Returns : String (database name)
Args : [optional] String (database name)
=cut
sub database {
my $self = shift;
return $self->{'_database'} = shift if @_;
return $self->{'_database'};
}
=head2 query_accession
Title : query_accession
Usage : my $acc = $parser->query_accession();
Function: Get/Set query (model) accession; RNAMotif currently does not output
the accession number
Returns : String (accession)
Args : [optional] String (accession)
=cut
sub query_accession {
my $self = shift;
return $self->{'_query_accession'} = shift if @_;
return $self->{'_query_accession'};
}
=head2 algorithm_version
Title : algorithm_version
Usage : my $ver = $parser->algorithm_version();
Function: Get/Set algorithm version (not defined in RNAMotif output)
Returns : String (accession)
Args : [optional] String (accession)
=cut
sub algorithm_version {
my $self = shift;
return $self->{'_algorithm'} = shift if @_;
return $self->{'_algorithm'};
}
=head2 hsp_minscore
Title : hsp_minscore
Usage : my $cutoff = $parser->hsp_minscore();
Function: Get/Set min score cutoff (for generating Hits/HSPs).
Returns : score (number)
Args : [optional] score (number)
Note : Cannot be set along with hsp_maxscore()
=cut
sub hsp_minscore {
my ($self, $score) = shift;
$self->throw('Minscore not set to a number') if
($score && $score !~ m{[0-9.]+});
return $self->{'_hsp_minscore'} = shift if @_;
return $self->{'_hsp_minscore'};
}
=head2 hsp_maxscore
Title : hsp_maxscore
Usage : my $cutoff = $parser->hsp_maxscore();
Function: Get/Set max score cutoff (for generating Hits/HSPs).
Returns : score (number)
Args : [optional] score (number)
Note : Cannot be set along with hsp_minscore()
=cut
sub hsp_maxscore {
my ($self, $score) = shift;
$self->throw('Maxscore not set to a number') if
($score && $score !~ m{[0-9.]+});
return $self->{'_hsp_maxscore'} = shift if @_;
return $self->{'_hsp_maxscore'};
}
=head2 structure_symbols
Title : structure_symbols
Usage : my $hashref = $parser->structure_symbols();
Function: Get/Set RNA structure symbols
Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)
: default = < (5-prime)
> (3-prime)
. (single-strand)
? (unknown)
Args : Hash ref of substitute delimiters, using above keys.
=cut
sub structure_symbols {
my ($self, $delim) = @_;
if ($delim) {
if (ref($delim) =~ m{HASH}) {
my %data = %{ $delim };
for my $d (@VALID_SYMBOLS) {
if ( exists $data{$d} ) {
$self->{'_delimiter'}->{$d} = $data{$d};
}
}
} else {
$self->throw("Args to helix_delimiters() should be in a hash reference");
}
}
return $self->{'_delimiter'};
}
#Private methods
=head2 _motif2meta
Title : _motif2meta
Usage : my ($rna, $meta) = $parser->_motif2meta($str, $descr);
Function: Creates meta string from sequence and descriptor
Returns : array of sequence, meta strings
Args : Array of string data and descriptor data
Note: This is currently a quick and simple way of making simple
RNA structures (stem-loops, helices, etc) from RNAMotif descriptor
data in the output file. It does not currently work with pseudoknots,
triplets, G-quartets, or other more complex RNA structural motifs.
=cut
sub _motif2meta {
my ($self, $str, $descriptor) = @_;
my ($rna, $meta);
my @desc_el = split ' ',$descriptor;
my @seq_el = split ' ',$str;
my $symbol = $self->structure_symbols();
if ($#desc_el != $#seq_el) {
$self->throw("Descriptor elements and seq elements do not match");
}
while (@desc_el) {
my $struct;
my ($seq, $motif) = (shift @seq_el, shift @desc_el);
$struct = (index($motif,'h5') == 0) ? $symbol->{'5-prime'} :
(index($motif,'h3') == 0) ? $symbol->{'3-prime'} :
(index($motif,'ss') == 0) ? $symbol->{'single-strand'} :
(index($motif,'ctx')== 0) ? $symbol->{'single-strand'} :
$symbol->{'unknown'};
$meta .= $struct x (length($seq));
$rna .= $seq;
}
return ($rna, $meta);
}
1;