Bio::SearchIO infernal
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Summary
Bio::SearchIO::infernal - SearchIO-based Infernal parser
Package variables
Privates (from "my" definitions)
$MINSCORE = 0
%STRUCTURE_SYMBOLS = ( '5-prime' => '<', '3-prime' => '>', 'single-strand' => ':', 'unknown' => '?', 'gap' => '.' )
$DEFAULT_VERSION = '1.0'
@VALID_SYMBOLS = qw(5-prime 3-prime single-strand unknown gap)
$DEFAULT_ALGORITHM = 'cmsearch'
Included modules
Data::Dumper
Inherit
Bio::SearchIO
Synopsis
  my $parser = Bio::SearchIO->new(-format => 'infernal',
-file => 'purine.inf');
while( my $result = $parser->next_result ) {
# general result info, such as model used, Infernal version
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
# ...
}
}
}
Description
This is a SearchIO-based parser for Infernal output from the cmsearch program.
It currently parses cmsearch output for Infernal versions 0.7-1.0; older
versions may work but will not be supported.
As the first stable version has been released (and output has stabilized) it is
highly recommended that users upgrade to using the latest Infernal release.
Support for the older pre-v.1 developer releases will be dropped for future core
1.6 releases.
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
modelDescriptionCode
databaseDescriptionCode
algorithmDescriptionCode
query_accessionDescriptionCode
query_descriptionDescriptionCode
hsp_minscoreDescriptionCode
convert_metaDescriptionCode
versionDescriptionCode
structure_symbolsDescriptionCode
simple_metaDescriptionCode
_parse_latest
No description
Code
_parse_pre
No description
Code
_parse_old
No description
Code
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
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)
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)
algorithmcodeprevnextTop
 Title   : algorithm
Usage : my $algorithm = $parser->algorithm();
Function: Get/Set algorithm; current versions of Infernal do not output
the algorithm name
Returns : String (algorithm name)
Args : [optional] String (algorithm name)
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)
query_descriptioncodeprevnextTop
 Title   : query_description
Usage : my $acc = $parser->query_description();
Function: Get/Set query (model) description; Infernal currently does not output
the Rfam description
Returns : String (description)
Args : [optional] String (description)
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)
convert_metacodeprevnextTop
 Title   : convert_meta
Usage : $parser->convert_meta(1);
Function: Get/Set boolean flag for converting Infernal WUSS format
to a simple bracketed format (simple WUSS by default)
Returns : boolean flag (TRUE or FALSE)
Args : [optional] boolean (eval's to TRUE or FALSE)
versioncodeprevnextTop
 Title   : version
Usage : $parser->version();
Function: Set the Infernal cmsearch version
Returns : version
Args : [optional] version
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)
. (gap)
Args : Hash ref of substitute delimiters, using above keys.
simple_metacodeprevnextTop
 Title   : simple_meta
Usage : my $string = $parser->simple_meta($str);
Function: converts more complex WUSS meta format into simple bracket format
using symbols defined in structure_symbols()
Returns : converted string
Args : [required] string to convert
Note : This is a very simple conversion method to get simple bracketed
format from Infernal data. If the convert_meta() flag is set,
this is the method used to convert the strings.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my ($model, $database, $convert, $symbols, $cutoff,
        $desc, $accession, $algorithm, $version) =
        $self->_rearrange([qw(MODEL
                          DATABASE
                          CONVERT_META
                          SYMBOLS
                          HSP_MINSCORE
                          QUERY_DESC
                          QUERY_ACC
                          ALGORITHM
                          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
        )
    );
	
    defined $model     && $self->model($model);
    defined $database  && $self->database($database);
    defined $accession && $self->query_accession($accession);
    defined $convert   && $self->convert_meta($convert);
    defined $desc      && $self->query_description($desc);
    
    $version ||= $DEFAULT_VERSION;
    $self->version($version);
    $symbols ||=\% STRUCTURE_SYMBOLS;
    $self->structure_symbols($symbols);
    $cutoff ||= $MINSCORE;
    $self->hsp_minscore($cutoff);
    $algorithm ||= $DEFAULT_ALGORITHM;
    $self->algorithm($algorithm);
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    unless (exists $self->{'_handlerset'}) {
        my $line;
        while ($line = $self->_readline) {
            # advance to first line
next if $line =~ m{^\s*$}; # newer output starts with model name
if ($line =~ m{^\#\s+cmsearch\s}) { $self->{'_handlerset'} = 'latest'; } elsif ($line =~ m{^CM\s\d+:}) { $self->{'_handlerset'} = 'pre-1.0'; } else { $self->{'_handlerset'} ='old'; } last; } $self->_pushback($line); #if ($self->{'_handlerset'} ne '1.0') {
# $self->deprecated(
# -message => "Parsing of Infernal pre-1.0 release is deprecated;\n".
# "upgrading to Infernal 1.0 or above is highly recommended",
# -version => 1.007);
#}
} return ($self->{'_handlerset'} eq 'latest') ? $self->_parse_latest : ($self->{'_handlerset'} eq 'pre-1.0') ? $self->_parse_pre : $self->_parse_old;
}
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'};
}
modeldescriptionprevnextTop
sub model {
    my $self = shift;
    return $self->{'_model'} = shift if @_;
    return $self->{'_model'};
}
databasedescriptionprevnextTop
sub database {
    my $self = shift;
    return $self->{'_database'} = shift if @_;
    return $self->{'_database'};
}
algorithmdescriptionprevnextTop
sub algorithm {
    my $self = shift;
    return $self->{'_algorithm'} = shift if @_;
    return $self->{'_algorithm'};
}
query_accessiondescriptionprevnextTop
sub query_accession {
    my $self = shift;
    return $self->{'_query_accession'} = shift if @_;
    return $self->{'_query_accession'};
}
query_descriptiondescriptionprevnextTop
sub query_description {
    my $self = shift;
    return $self->{'_query_description'} = shift if @_;
    return $self->{'_query_description'};
}
hsp_minscoredescriptionprevnextTop
sub hsp_minscore {
    my $self = shift;
    return $self->{'_hsp_minscore'} = shift if @_;
    return $self->{'_hsp_minscore'};
}
convert_metadescriptionprevnextTop
sub convert_meta {
    my $self = shift;
    return $self->{'_convert_meta'} = shift if @_;
    return $self->{'_convert_meta'};
}
versiondescriptionprevnextTop
sub version {
    my $self = shift;
    return $self->{'_version'} = shift if @_;
    return $self->{'_version'};
}
structure_symbolsdescriptionprevnextTop
sub structure_symbols {
    my ($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 $self->{'_delimiter'};
}
simple_metadescriptionprevnextTop
sub simple_meta {
    my ($self, $str) = @_;
    $self->throw("No string arg sent!") if !$str;
    my $structs = $self->structure_symbols();
    my ($ls, $rs, $ss, $unk, $gap) = ($structs->{'5-prime'}, $structs->{'3-prime'},
                                $structs->{'single-strand'}, $structs->{'unknown'},
                                $structs->{'gap'});
    $str =~ s{[\(\<\[\{]}{$ls}g;
    $str =~ s{[\)\>\]\}]}{$rs}g;
    $str =~ s{[:,_-]}{$ss}g;
    $str =~ s{\.}{$gap}g;
    # unknown not handled yet
return $str; } ## private methods
# this is a hack which guesses the format and sets the handler for parsing in
# an instance; it'll be taken out when infernal 1.0 is released
}
_parse_latestdescriptionprevnextTop
sub _parse_latest {
    my ($self) = @_;
    my $seentop = 0;
    local $/ = "\n";
    my ($accession, $description) = ($self->query_accession, $self->query_description);
    my ($maxscore, $mineval, $minpval);
    $self->start_document();
    my ($lasthit, $lastscore, $lasteval, $lastpval, $laststart, $lastend);
    PARSER:
    while (my $line = $self->_readline) {
        next if $line =~ m{^\s+$};
        # stats aren't parsed yet...
if ($line =~ m{^\#\s+cmsearch}xms) { $seentop = 1; $self->start_element({'Name' => 'Result'}); $self->element_hash({ 'Infernal_program' => 'CMSEARCH' }); } elsif ($line =~ m{^\#\sINFERNAL\s+(\d+\.\d+)}xms) { $self->element_hash({ 'Infernal_version' => $1, }); } elsif ($line =~ m{^\#\scommand:.*?\s(\S+)$}xms) { $self->element_hash({ 'Infernal_db' => $1, }); } elsif ($line =~ m{^\#\s+dbsize\(Mb\):\s+(\d+\.\d+)}xms) { # store absolute DB length
$self->element_hash({ 'Infernal_db-let' => $1 * 1e6 }); } elsif ($line =~ m{^CM(?:\s(\d+))?:\s*(\S+)}xms) { # not sure, but it's possible single reports may contain multiple
# models; if so, they should be rolled over into a new ResultI
#print STDERR "ACC: $accession\nDESC: $description\n";
$self->element_hash({ 'Infernal_query-def' => $2, # present in output now
'Infernal_query-acc' => $accession, 'Infernal_querydesc' => $description }); } elsif ($line =~ m{^>\s*(\S+)} ){ #$self->debug("Start Hit: Found hit:$1\n");
if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); ($maxscore, $minpval, $mineval) = undef; $self->end_element({'Name' => 'Hit'}); } $lasthit = $1; } elsif ($line =~ m{
^\sQuery\s=\s\d+\s-\s\d+,\s # Query start/end
Target\s=\s(\d+)\s-\s(\d+) # Target start/end
}xmso
) { # Query (model) start/end always the same, determined from
# the HSP length
($laststart, $lastend) = ($1, $2); #$self->debug("Found hit coords:$laststart - $lastend\n");
} elsif ($line =~ m{
^\sScore\s=\s([\d\.]+),\s # Score = Bitscore (for now)
(?:E\s=\s([\d\.e-]+),\s # E-val optional
P\s=\s([\d\.e-]+),\s)? # P-val optional
GC\s= # GC not captured
}xmso
) { ($lastscore, $lasteval, $lastpval) = ($1, $2, $3); #$self->debug(sprintf("Found hit data:Score:%s,Eval:%s,Pval:%s\n",$lastscore, $lasteval||'', $lastpval||''));
$maxscore ||= $lastscore; if ($lasteval && $lastpval) { $mineval ||= $lasteval; $minpval ||= $lastpval; $mineval = ($mineval > $lasteval) ? $lasteval : $mineval; $minpval = ($minpval > $lastpval) ? $lastpval : $minpval; } $maxscore = ($maxscore < $lastscore) ? $lastscore : $maxscore; if (!$self->within_element('hit')) { my ($gi, $acc, $ver) = $self->_get_seq_identifiers($lasthit); $self->start_element({'Name' => 'Hit'}); $self->element_hash({ 'Hit_id' => $lasthit, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $lasthit, 'Hit_gi' => $gi }); } if (!$self->in_element('hsp')) { $self->start_element({'Name' => 'Hsp'}); } # hsp is similar to older output
} elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP
$self->_pushback($line); # set up for loop
#$self->debug("Start HSP\n");
# what is length of the gap to the structure data?
my $offset = length($1); my ($ct, $strln) = 0; my $hsp; HSP: my %hsp_key = ('0' => 'meta', '1' => 'query', '2' => 'midline', '3' => 'hit'); HSP: while (defined ($line = $self->_readline)) { chomp $line; next if (!$line); # toss empty lines
# next if $line =~ m{^\s*$}; # toss empty lines
# it is possible to have homology lines consisting
# entirely of spaces if the subject has a large
# insertion where nothing matches the model
# exit loop if at end of file or upon next hit/HSP
if ($line =~ m{^\s{0,2}\S+}) { $self->_pushback($line); last HSP; } # iterate to keep track of each line (4 lines per hsp block)
my $iterator = $ct % 4; # strlen set only with structure lines (proper length)
$strln = length($line) if $iterator == 0; # only grab the data needed (hit start and stop in hit line above)
my $data = substr($line, $offset, $strln-$offset); $hsp->{ $hsp_key{$iterator} } .= $data; $ct++; } # query start, end are from the actual query length (entire hit is
# mapped to CM data, so all CM data is represented)
# works for now...
if ($self->in_element('hsp')) { # In some cases with HSPs unaligned residues are present in
# the hit or query (Ex: '*[ 8]*' is 8 unaligned residues).
# This info needs to be passed on unmodifed to the HSP class
# and handled there as it is subjectively changed based on
# use.
my $strlen = 0; # catch any insertions and add them into the actual length
while ($hsp->{'query'} =~ m{\*\[\s*(\d+)\s*\]\*}g) { $strlen += $1; } # add on the actual residues
$strlen += $hsp->{'query'} =~ tr{A-Za-z}{A-Za-z}; my $metastr = ($self->convert_meta) ? ($self->simple_meta($hsp->{'meta'})) : $hsp->{'meta'}; $self->element_hash( {'Hsp_stranded' => 'HIT', 'Hsp_qseq' => $hsp->{'query'}, 'Hsp_hseq' => $hsp->{'hit'}, 'Hsp_midline' => $hsp->{'midline'}, 'Hsp_structure' => $metastr, 'Hsp_query-from' => 1, 'Infernal_query-len' => $strlen, 'Hsp_query-to' => $strlen, 'Hsp_hit-from' => $laststart, 'Hsp_hit-to' => $lastend, 'Hsp_score' => $lastscore, 'Hsp_bit-score' => $lastscore, }); $self->element_hash( {'Hsp_evalue' => $lasteval, 'Hsp_pvalue' => $lastpval, }) if ($lasteval && $lastpval); $self->end_element({'Name' => 'Hsp'}); } # result now ends with // and 'Fin'
} elsif ($line =~ m{^//}xms ) { if ($self->within_element('result') && $seentop) { if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); # don't know where to put minpval yet
$self->element_hash({'Hit_signif' => $mineval}) if $mineval; $self->element_hash({'Hit_p' => $minpval}) if $minpval; $self->end_element({'Name' => 'Hit'}); } last PARSER; } } } $self->within_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'Result' } ) if $seentop; return $self->end_document(); } # cmsearch 0.81 (pre-1.0)
}
_parse_predescriptionprevnextTop
sub _parse_pre {
    my ($self) = @_;
    my $seentop = 0;
    local $/ = "\n";
    my ($accession, $db, $algorithm, $description, $version) =
       ($self->query_accession, $self->database, $self->algorithm,
        $self->query_description, '0.81');
    my ($maxscore, $mineval, $minpval);
    $self->start_document();
    my ($lasthit, $lastscore, $lasteval, $lastpval, $laststart, $lastend);
    PARSER:
    while (my $line = $self->_readline) {
        next if $line =~ m{^\s+$};
        # stats aren't parsed yet...
if ($line =~ m{CM\s\d+:\s*(\S+)}xms) { #$self->debug("Start Result: Found model:$1\n");
if (!$self->within_element('result')) { $seentop = 1; $self->start_element({'Name' => 'Result'}); $self->element_hash({ 'Infernal_program' => $algorithm, 'Infernal_query-def' => $1, # present in output now
'Infernal_query-acc' => $accession, 'Infernal_querydesc' => $description, 'Infernal_db' => $db }); } } elsif ($line =~ m{^>\s*(\S+)} ){ #$self->debug("Start Hit: Found hit:$1\n");
if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); ($maxscore, $minpval, $mineval) = undef; $self->end_element({'Name' => 'Hit'}); } $lasthit = $1; } elsif ($line =~ m{
^\sQuery\s=\s\d+\s-\s\d+,\s # Query start/end
Target\s=\s(\d+)\s-\s(\d+) # Target start/end
}xmso
) { # Query (model) start/end always the same, determined from
# the HSP length
($laststart, $lastend) = ($1, $2); #$self->debug("Found hit coords:$laststart - $lastend\n");
} elsif ($line =~ m{
^\sScore\s=\s([\d\.]+),\s # Score = Bitscore (for now)
(?:E\s=\s([\d\.e-]+),\s # E-val optional
P\s=\s([\d\.e-]+),\s)? # P-val optional
GC\s= # GC not captured
}xmso
) { ($lastscore, $lasteval, $lastpval) = ($1, $2, $3); #$self->debug(sprintf("Found hit data:Score:%s,Eval:%s,Pval:%s\n",$lastscore, $lasteval||'', $lastpval||''));
$maxscore ||= $lastscore; if ($lasteval && $lastpval) { $mineval ||= $lasteval; $minpval ||= $lastpval; $mineval = ($mineval > $lasteval) ? $lasteval : $mineval; $minpval = ($minpval > $lastpval) ? $lastpval : $minpval; } $maxscore = ($maxscore < $lastscore) ? $lastscore : $maxscore; if (!$self->within_element('hit')) { my ($gi, $acc, $ver) = $self->_get_seq_identifiers($lasthit); $self->start_element({'Name' => 'Hit'}); $self->element_hash({ 'Hit_id' => $lasthit, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $lasthit, 'Hit_gi' => $gi }); } if (!$self->in_element('hsp')) { $self->start_element({'Name' => 'Hsp'}); } # hsp is similar to older output
} elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP
$self->_pushback($line); # set up for loop
#$self->debug("Start HSP\n");
# what is length of the gap to the structure data?
my $offset = length($1); my ($ct, $strln) = 0; my $hsp; HSP: my %hsp_key = ('0' => 'meta', '1' => 'query', '2' => 'midline', '3' => 'hit'); HSP: while (defined ($line = $self->_readline)) { chomp $line; next if (!$line); # toss empty lines
# next if $line =~ m{^\s*$}; # toss empty lines
# it is possible to have homology lines consisting
# entirely of spaces if the subject has a large
# insertion where nothing matches the model
# exit loop if at end of file or upon next hit/HSP
if ($line =~ m{^\s{0,2}\S+}) { $self->_pushback($line); last HSP; } # iterate to keep track of each line (4 lines per hsp block)
my $iterator = $ct%4; # strlen set only with structure lines (proper length)
$strln = length($line) if $iterator == 0; # only grab the data needed (hit start and stop in hit line above)
my $data = substr($line, $offset, $strln-$offset); $hsp->{ $hsp_key{$iterator} } .= $data; $ct++; } # query start, end are from the actual query length (entire hit is
# mapped to CM data, so all CM data is represented)
# works for now...
if ($self->in_element('hsp')) { my $strlen = $hsp->{'query'} =~ tr{A-Za-z}{A-Za-z}; my $metastr; $metastr = ($self->convert_meta) ? ($self->simple_meta($hsp->{'meta'})) : ($hsp->{'meta'}); $self->element_hash( {'Hsp_stranded' => 'HIT', 'Hsp_qseq' => $hsp->{'query'}, 'Hsp_hseq' => $hsp->{'hit'}, 'Hsp_midline' => $hsp->{'midline'}, 'Hsp_structure' => $metastr, 'Hsp_query-from' => 1, 'Infernal_query-len' => $strlen, 'Hsp_query-to' => $strlen, 'Hsp_hit-from' => $laststart, 'Hsp_hit-to' => $lastend, 'Hsp_score' => $lastscore, 'Hsp_bit-score' => $lastscore, }); $self->element_hash( {'Hsp_evalue' => $lasteval, 'Hsp_pvalue' => $lastpval, }) if ($lasteval && $lastpval); $self->end_element({'Name' => 'Hsp'}); } # result now ends with // and 'Fin'
} elsif ($line =~ m{^//}xms ) { if ($self->within_element('result') && $seentop) { $self->element( {'Name' => 'Infernal_version', 'Data' => $version} ); if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); # don't know where to put minpval yet
$self->element_hash({'Hit_signif' => $mineval}) if $mineval; $self->end_element({'Name' => 'Hit'}); } last PARSER; } } } $self->within_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'Result' } ) if $seentop; return $self->end_document(); } # cmsearch 0.72 and below; will likely be dropped when Infernal 1.0 is released
}
_parse_olddescriptionprevnextTop
sub _parse_old {
    my ($self) = @_;
    my $seentop = 0;
    local $/ = "\n";
    my ($accession, $db, $algorithm, $model, $description, $version) =
       ($self->query_accession, $self->database, $self->algorithm,
        $self->model, $self->query_description, $self->version);
    my $maxscore;
    my $cutoff = $self->hsp_minscore;
    $self->start_document();
    local ($_);
    my $line;
    my ($lasthit, $lastscore, $laststart, $lastend);
    my $hitline;
    PARSER:
    while ( defined( $line = $self->_readline ) ) {
        next if $line =~ m{^\s+$};
        # bypass this for now...
next if $line =~ m{^HMM\shit}; # pre-0.81
if ($line =~ m{^sequence:\s+(\S+)} ){ if (!$self->within_element('result')) { $seentop = 1; $self->start_element({'Name' => 'Result'}); $self->element_hash({ 'Infernal_program' => $algorithm, 'Infernal_query-def' => $model, 'Infernal_query-acc' => $accession, 'Infernal_querydesc' => $description, 'Infernal_db' => $db }); } if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); $maxscore = undef; $self->end_element({'Name' => 'Hit'}); } $lasthit = $1; } elsif ($line =~ m{^hit\s+\d+\s+:\s+(\d+)\s+(\d+)\s+(\d+\.\d+)\s+bits}xms) { ($laststart, $lastend, $lastscore) = ($1, $2, $3); $maxscore = $lastscore unless $maxscore; if ($lastscore > $cutoff) { if (!$self->within_element('hit')) { my ($gi, $acc, $ver) = $self->_get_seq_identifiers($lasthit); $self->start_element({'Name' => 'Hit'}); $self->element_hash({ 'Hit_id' => $lasthit, 'Hit_accession' => $ver ? "$acc.$ver" : $acc ? $acc : $lasthit, 'Hit_gi' => $gi }); } # necessary as infernal 0.71 has repeated hit line
if (!$self->in_element('hsp')) { $self->start_element({'Name' => 'Hsp'}); } $maxscore = ($maxscore < $lastscore) ? $lastscore : $maxscore; } } elsif ($line =~ m{^(\s+)[<>\{\}\(\)\[\]:_,-\.]+}xms) { # start of HSP
$self->_pushback($line); # set up for loop
# what is length of the gap to the structure data?
my $offset = length($1); my ($ct, $strln) = 0; my $hsp; HSP: my %hsp_key = ('0' => 'meta', '1' => 'query', '2' => 'midline', '3' => 'hit'); HSP: while ($line = $self->_readline) { next if $line =~ m{^\s*$}; # toss empty lines
chomp $line; # exit loop if at end of file or upon next hit/HSP
if (!defined($line) || $line =~ m{^\S+}) { $self->_pushback($line); last HSP; } # iterate to keep track of each line (4 lines per hsp block)
my $iterator = $ct%4; # strlen set only with structure lines (proper length)
$strln = length($line) if $iterator == 0; # only grab the data needed (hit start and stop in hit line above)
my $data = substr($line, $offset, $strln-$offset); $hsp->{ $hsp_key{$iterator} } .= $data; $ct++; } # query start, end are from the actual query length (entire hit is
# mapped to CM data, so all CM data is represented)
# works for now...
if ($self->in_element('hsp')) { my $strlen = $hsp->{'query'} =~ tr{A-Za-z}{A-Za-z}; my $metastr; # Ugh...these should be passed in a hash
$metastr = ($self->convert_meta) ? ($self->simple_meta($hsp->{'meta'})) : ($hsp->{'meta'}); $self->element_hash( {'Hsp_stranded' => 'HIT', 'Hsp_qseq' => $hsp->{'query'}, 'Hsp_hseq' => $hsp->{'hit'}, 'Hsp_midline' => $hsp->{'midline'}, 'Hsp_structure' => $metastr, 'Hsp_query-from' => 1, 'Infernal_query-len' => $strlen, 'Hsp_query-to' => $strlen, 'Hsp_hit-from' => $laststart, 'Hsp_hit-to' => $lastend, 'Hsp_score' => $lastscore, 'Hsp_bit-score' => $lastscore }); $self->end_element({'Name' => 'Hsp'}); } } elsif ($line =~ m{^memory}xms || $line =~ m{^CYK\smemory}xms ) { if ($self->within_element('result') && $seentop) { $self->element( {'Name' => 'Infernal_version', 'Data' => $version} ); if ($self->in_element('hit')) { $self->element_hash({'Hit_score' => $maxscore, 'Hit_bits' => $maxscore}); $self->end_element({'Name' => 'Hit'}); } last PARSER; } } } $self->within_element('hit') && $self->end_element( { 'Name' => 'Hit' } ); $self->end_element( { 'Name' => 'Result' } ) if $seentop; return $self->end_document(); } 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
CONTRIBUTORSTop
  Jeffrey Barrick, Michigan State University
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 => 'infernal'
-model => query model (Rfam ID) (default undef)
-database => database name (default undef)
-query_acc => query accession, eg. Rfam accession RF####
-query_desc => query description, eg. Rfam description
-hsp_minscore => minimum HSP score cutoff
-convert_meta => boolean, set to convert meta string to simple WUSS format
-symbols => hash ref of structure symbols to use
(default symbols in %STRUCTURE_SYMBOLS hash)