Bio::SearchIO erpin
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::SearchIO::erpin - SearchIO-based ERPIN parser
Package variables
Privates (from "my" definitions)
$MINSCORE = 0
$DEFAULT_VERSION = '4.2.5'
%MODEMAP = ( 'Result' => '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_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_structure' => 'HSP-meta', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_stranded' => 'HSP-stranded', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_gi' => 'HIT-ncbi_gi', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_signif' => 'HIT-significance', 'Hit_score' => 'HIT-score', 'Hit_bits' => 'HIT-bits', 'ERPIN_program' => 'RESULT-algorithm_name', 'ERPIN_version' => 'RESULT-algorithm_version', 'ERPIN_query-def'=> 'RESULT-query_name', 'ERPIN_query-len'=> 'RESULT-query_length', 'ERPIN_query-acc'=> 'RESULT-query_accession', 'ERPIN_querydesc'=> 'RESULT-query_description', 'ERPIN_db' => 'RESULT-database_name', 'ERPIN_db-len' => 'RESULT-database_entries', 'ERPIN_db-let' => 'RESULT-database_letters', 'Parameters_cutoff' => { 'RESULT-parameters' => 'cutoff' }, 'Parameters_expect' => { 'RESULT-parameters' => 'expect' }, 'Parameters_include' => { 'RESULT-parameters' => 'include' }, 'Parameters_sc-match' => { 'RESULT-parameters' => 'match' }, 'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch' }, 'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen' }, 'Parameters_gap-extend' => { 'RESULT-parameters' => 'gapext' }, 'Parameters_filter' => { 'RESULT-parameters' => 'filter' }, 'Parameters_allowgaps' => { 'RESULT-parameters' => 'allowgaps' }, 'Parameters_full_dbpath' => { 'RESULT-parameters' => 'full_dbpath' }, 'Statistics_db-let' => { 'RESULT-statistics' => 'dbletters' }, )
$DEFAULT_ALGORITHM = 'erpin'
Included modules
Data::Dumper
Inherit
Bio::SearchIO
Synopsis
  # do not call this module directly. Use Bio::SearchIO.
Description
This is an experimental SearchIO-based parser for output from
the erpin program. It currently parses erpin output for ERPIN
versions 4.2.5 and above; older versions may work but will not be supported.
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
query_accessionDescriptionCode
hsp_minscoreDescriptionCode
algorithm_versionDescriptionCode
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
query_accessioncodeprevnextTop
 Title   : query_accession
Usage : my $acc = $parser->query_accession();
Function: Get/Set query (model) accession; Infernal currently does not output
the accession number (Rfam accession #)
Returns : String (accession)
Args : [optional] String (accession)
hsp_minscorecodeprevnextTop
 Title   : hsp_minscore
Usage : my $cutoff = $parser->hsp_minscore();
Function: Get/Set min bit score cutoff (for generating Hits/HSPs)
Returns : score (number)
Args : [optional] score (number)
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)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my ($cutoff, $accession, $version) =
       $self->_rearrange([qw(HSP_MINSCORE QUERY_ACC VERSION)],@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()
        )
    );
    $accession && $self->query_accession($accession);
    $cutoff ||= $MINSCORE;
    $self->hsp_minscore($cutoff);
    $version ||= $DEFAULT_VERSION;
    $self->algorithm_version($version);
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    my $seentop = 0;
    local $/ = "\n";
    local $_;
    my $accession = $self->query_accession;
    my $minscore = $self->hsp_minscore;
    my $version = $self->algorithm_version;
    my $verbose = $self->verbose;    # cache for speed?
$self->start_document(); my ($lasthit, $lastscore, $lastlen, $lasteval); #my $hitline;
PARSER: while ( defined( my $line = $self->_readline ) ) { next if $line =~ m{^\s*$}; if ($line =~ m{^Training\sset:\s+"(.*)"}xmso) { if ($seentop) { $self->_pushback($line); last PARSER; } $self->start_element({'Name' => 'Result'}); $self->element_hash( { 'ERPIN_query-def' => $1, 'ERPIN_program' =>'erpin', 'ERPIN_version' => $version, 'ERPIN_query-acc' => $accession, }); $seentop = 1; # parse rest of header here
HEADER: while (defined ($line = $self->_readline) ) { next if $line =~ m{^\s*$}; if (index($line, '>') == 0 || index($line, '-------- at level 1 --------') == 0) { $self->_pushback($line); last HEADER; } if ($line =~ m{^\s+(\d+\ssequences\sof\slength\s\d+)}xmso) { $self->element( {'Name' => 'ERPIN_querydesc', 'Data' => $1} ); } elsif ($line =~ m{^Cutoff:\s+(\S+)}xmso) { $self->element( {'Name' => 'Parameters_cutoff', 'Data' => $1} ); } elsif ($line =~ m{^Database:\s+"(.*)"}xmso) { $self->element( {'Name' => 'ERPIN_db', 'Data' => $1} ); } elsif ($line =~ m{^\s+(\d+)\snucleotides\sto\sbe\sprocessed\sin\s(\d+)\ssequences}xmso) { $self->element_hash( {'ERPIN_db-len' => $2, 'ERPIN_db-let' => $1} ); } elsif ($line =~ m{^E-value\sat\scutoff\s\S+\sfor\s\S+\sdouble\sstrand\sdata:\s+(\S+)}xmso) { $self->element( {'Name' => 'Parameters_expect', 'Data' => $1} ); } elsif ($line =~ m{^\s+(ATGC\sratios:\s+(?:\S+\s+\S+\s+\S+\s+\S+))}) { $self->element( {'Name' => 'Statistics_db-let', 'Data' => $1} ); } } } elsif ($line =~ m{^>(\S+)\s+(.*)}xmso ) { my ($id, $desc) = ($1, $2); chomp $desc; # desc line is repeated for each strand, so must check
# prior to starting a new hit
if (!$lasthit || $id ne $lasthit) { if ($self->within_element('hit') ) { $self->element_hash({ 'Hit_signif' => $lasteval, 'Hit_score' => $lastscore, 'Hit_bits' => $lastscore }); $self->end_element({'Name' => 'Hit'}); } $self->start_element({'Name' => 'Hit'}); my ($gi, $acc, $ver) = $self->_get_seq_identifiers($id); $self->element_hash({ 'Hit_id' => $id, 'Hit_gi' => $gi, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $id, 'Hit_def' => $desc }); } $lasthit = $id; } elsif ( (index($line, 'FW') == 0) || (index($line, 'RC') == 0)) { my ($str, $hn, $pos, $score, $eval) = split ' ', $line; if ($minscore < $score) { $self->start_element({'Name' => 'Hsp'}); my ($start, $end) = split m{\.\.}, $pos, 2; ($start, $end) = ($end, $start) if ($str eq 'RC'); $line = $self->_readline; chomp $line; $self->element_hash({ 'Hsp_stranded' => 'HIT', 'Hsp_hit-from' => $start, 'Hsp_hit-to' => $end, 'Hsp_score' => $score, 'Hsp_bit-score' => $score, 'Hsp_evalue' => $eval, 'Hsp_query-from' => 1, 'Hsp_query-to' => length($line), 'Hsp_align-len' => length($line), 'Hsp_hseq' =>$line }); $self->end_element({'Name' => 'Hsp'}); $lastscore = $score if (!$lastscore || $lastscore < $score); $lasteval = $eval if (!$lasteval || $lasteval > $eval); } } else { #$self->debug("Dropped data: $line");
} } if ($seentop) { if ($self->within_element('hit')) { $self->element_hash({ 'Hit_signif' => $lasteval, 'Hit_score' => $lastscore, 'Hit_bits' => $lastscore }); $self->end_element({'Name' => 'Hit'}); } $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'};
}
query_accessiondescriptionprevnextTop
sub query_accession {
    my $self = shift;
    return $self->{'_query_accession'} = shift if @_;
    return $self->{'_query_accession'};
}
hsp_minscoredescriptionprevnextTop
sub hsp_minscore {
    my $self = shift;
    return $self->{'_hsp_minscore'} = shift if @_;
    return $self->{'_hsp_minscore'};
}
algorithm_versiondescriptionprevnextTop
sub algorithm_version {
    my $self = shift;
    return $self->{'_algorithm'} = shift if @_;
    return $self->{'_algorithm'};
}

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::infernal->new();
Function: Builds a new Bio::SearchIO::infernal object
Returns : Bio::SearchIO::infernal
Args : -fh/-file => cmsearch (infernal) filename
-format => 'erpin'
-algorithm => algorithm (default 'Infernal')
-query_acc => query accession, eg. Rfam accession (default undef)
-hsp_minscore => minimum HSP score cutoff
-version => ERPIN version (not reported in output)