Bio::SearchIO
rnamotif
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Summary
Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser
Package variables
Privates (from "my" definitions)
%STRUCTURE_SYMBOLS = ( '5-prime' => '<', '3-prime' => '>', 'single-strand' => '.', 'unknown' => '?' )
@VALID_SYMBOLS = qw(5-prime 3-prime single-strand unknown)
$DEFAULT_VERSION = '3.0.3'
%MODEMAP = ( 'Result' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' )
%MAPPING = ( 'Hsp_score' => 'HSP-score', 'Hsp_custom-data' => 'HSP-custom_score', '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_hseq' => 'HSP-hit_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_structure' => 'HSP-meta', 'Hsp_stranded' => 'HSP-stranded', 'Hit_id' => 'HIT-name', 'Hit_accession' => 'HIT-accession', 'Hit_gi' => 'HIT-ncbi_gi', 'Hit_def' => 'HIT-description', 'Hit_score' => 'HIT-score', 'RNAMotif_program' => 'RESULT-algorithm_name', 'RNAMotif_version' => 'RESULT-algorithm_version', 'RNAMotif_query-def'=> 'RESULT-query_name', 'RNAMotif_query-acc'=> 'RESULT-query_accession', 'RNAMotif_querydesc'=> 'RESULT-query_description', 'RNAMotif_db' => 'RESULT-database_name', )
Inherit
Synopsis
# do not call this module directly. Use Bio::SearchIO.
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.
Methods
Methods description
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 |
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' |
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' |
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' |
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 |
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string |
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 |
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 |
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none |
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none |
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none |
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) |
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() |
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) |
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) |
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) |
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() |
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() |
Title : structure_symbols
Usage : my $hashref = $parser->structure_symbols();
Function: Get/Set RNA structure symbols
Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)
: default = < (5-prime)
> (3-prime)
. (single-strand)
? (unknown)
Args : Hash ref of substitute delimiters, using above keys. |
Title : _motif2meta
Usage : my ($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. |
Methods code
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);} | sub next_result
{ my ($self) = @_;
my $seentop = 0;
local $/ = "\n";
local $_;
my ($rm, $d, $descriptor, $file, $oktobuild);
my ($hitid, $hitdesc, $hspid, $lastid, $lastscore);
my $sprintf;
my ($accession, $db, $model) =
($self->query_accession, $self->database, $self->model);
my $hsp_min = $self->hsp_minscore;
my $hsp_max = $self->hsp_maxscore;
my $version = $self->algorithm_version;
my $laststart;
my $verbose = $self->verbose;
$self->start_document();
PARSER:
while ( defined( my $line = $self->_readline ) ) {
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
});
$seentop = 1;
} elsif (index($line,'#RM descr') == 0) {
($rm, $d, $descriptor) = split ' ', $line, 3;
chomp $descriptor;
$self->{'_descriptor'} = $descriptor;
$self->element(
{'Name' => 'RNAMotif_querydesc',
'Data' => $descriptor}
);
} elsif(index($line,'#RM dfile') == 0) {
($rm, $d, $file) = split ' ', $line, 3;
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);
$score *= 1;
unless ($hitid eq $hspid) {
$self->throw("IDs do not match!");
}
if (!defined($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)) ) {
$oktobuild = 0;
} else {
$oktobuild = 1;
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 < $lastscore;
}
}
}
if ($oktobuild) {
my $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();} | sub start_element
{ my ( $self, $data ) = @_;
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 $rc;
if ($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'} = '';
$self->{'_result'} = $rc if ( defined $type && $type eq 'result' );
return $rc;} | sub element
{ my ( $self, $data ) = @_;
$self->characters($data);
$self->end_element($data);} | 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};
}
}
}} | sub characters
{ my ( $self, $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'};} | sub descriptor
{ my $self = shift;
return $self->{'_descriptor'} = shift if @_;
return $self->{'_descriptor'};} | sub model
{ shift->descriptor(@_) } | sub database
{ my $self = shift;
return $self->{'_database'} = shift if @_;
return $self->{'_database'};} | sub query_accession
{ my $self = shift;
return $self->{'_query_accession'} = shift if @_;
return $self->{'_query_accession'};} | sub algorithm_version
{ my $self = shift;
return $self->{'_algorithm'} = shift if @_;
return $self->{'_algorithm'};} | sub hsp_minscore
{ my ($self, $score) = shift;
$self->throw('Minscore not set to a number') if
($score && $score !~ m{[0-9.]+});
return $self->{'_hsp_minscore'} = shift if @_;
return $self->{'_hsp_minscore'};} | sub hsp_maxscore
{ my ($self, $score) = shift;
$self->throw('Maxscore not set to a number') if
($score && $score !~ m{[0-9.]+});
return $self->{'_hsp_maxscore'} = shift if @_;
return $self->{'_hsp_maxscore'};} | sub structure_symbols
{ my ($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 $self->{'_delimiter'};
}
} | sub _motif2meta
{ my ($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;} | General documentation
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
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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.
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/
Email cjfields-at-uiuc-dot-edu
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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)