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
Bio::SearchIO
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
_initialize
No description
Code
next_resultDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
element_hashDescriptionCode
charactersDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
result_countDescriptionCode
descriptorDescriptionCode
modelDescriptionCode
databaseDescriptionCode
query_accessionDescriptionCode
algorithm_versionDescriptionCode
hsp_minscoreDescriptionCode
hsp_maxscoreDescriptionCode
structure_symbolsDescriptionCode
_motif2metaDescriptionCode
Methods description
next_resultcode    nextTop
 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_elementcodeprevnextTop
 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_elementcodeprevnextTop
 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'
elementcodeprevnextTop
 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'
element_hashcodeprevnextTop
 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
characterscodeprevnextTop
 Title   : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
within_elementcodeprevnextTop
 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_elementcodeprevnextTop
 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
start_documentcodeprevnextTop
 Title   : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
end_documentcodeprevnextTop
 Title   : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
result_countcodeprevnextTop
 Title   : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
descriptorcodeprevnextTop
 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)
modelcodeprevnextTop
 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()
databasecodeprevnextTop
 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)
query_accessioncodeprevnextTop
 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)
algorithm_versioncodeprevnextTop
 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)
hsp_minscorecodeprevnextTop
 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()
hsp_maxscorecodeprevnextTop
 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()
structure_symbolscodeprevnextTop
 Title   : structure_symbols
Usage : my $hashref = $parser->structure_symbols();
Function: Get/Set RNA structure symbols
Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)
: default = < (5-prime)
> (3-prime)
. (single-strand)
? (unknown)
Args : Hash ref of substitute delimiters, using above keys.
_motif2metacodeprevnextTop
 Title   : _motif2meta
Usage : my ($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
_initializedescriptionprevnextTop
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);
}
next_resultdescriptionprevnextTop
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();
}
start_elementdescriptionprevnextTop
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; }
}
end_elementdescriptionprevnextTop
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;
}
elementdescriptionprevnextTop
sub element {
    my ( $self, $data ) = @_;
    # simple data calls (%MAPPING) do not need start_element
$self->characters($data); $self->end_element($data);
}
element_hashdescriptionprevnextTop
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};
            }
        }
    }
}
charactersdescriptionprevnextTop
sub characters {
    my ( $self, $data ) = @_;
    return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o );
    $self->{'_last_data'} = $data->{'Data'};
}
within_elementdescriptionprevnextTop
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;
}
in_elementdescriptionprevnextTop
sub in_element {
    my ( $self, $name ) = @_;
    return 0 if !defined $self->{'_elements'}->[0];
    return ( $self->{'_elements'}->[0] eq $name );
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'}   = {};
    $self->{'_result'}   = undef;
    $self->{'_elements'} = [];
}
end_documentdescriptionprevnextTop
sub end_document {
    my ($self) = @_;
    return $self->{'_result'};
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
descriptordescriptionprevnextTop
sub descriptor {
    my $self = shift;
    return $self->{'_descriptor'} = shift if @_;
    return $self->{'_descriptor'};
}
modeldescriptionprevnextTop
sub model {
 shift->descriptor(@_)
}
databasedescriptionprevnextTop
sub database {
    my $self = shift;
    return $self->{'_database'} = shift if @_;
    return $self->{'_database'};
}
query_accessiondescriptionprevnextTop
sub query_accession {
    my $self = shift;
    return $self->{'_query_accession'} = shift if @_;
    return $self->{'_query_accession'};
}
algorithm_versiondescriptionprevnextTop
sub algorithm_version {
    my $self = shift;
    return $self->{'_algorithm'} = shift if @_;
    return $self->{'_algorithm'};
}
hsp_minscoredescriptionprevnextTop
sub hsp_minscore {
    my ($self, $score) = shift;
    $self->throw('Minscore not set to a number') if
        ($score && $score !~ m{[0-9.]+});
    return $self->{'_hsp_minscore'} = shift if @_;
    return $self->{'_hsp_minscore'};
}
hsp_maxscoredescriptionprevnextTop
sub hsp_maxscore {
    my ($self, $score) = shift;
    $self->throw('Maxscore not set to a number') if
        ($score && $score !~ m{[0-9.]+});
    return $self->{'_hsp_maxscore'} = shift if @_;
    return $self->{'_hsp_maxscore'};
}
structure_symbolsdescriptionprevnextTop
sub structure_symbols {
    my ($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
}
_motif2metadescriptionprevnextTop
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
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 - Chris FieldsTop
Email cjfields-at-uiuc-dot-edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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)