Bio::SearchIO
erpin
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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
Inherit
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
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 : 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) |
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) |
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
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);} | 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;
$self->start_document();
my ($lasthit, $lastscore, $lastlen, $lasteval);
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,
});
$seentop = 1;
HEADER:
while (defined ($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 $desc;
if (!$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 > $eval);
}
} else {
}
}
if ($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();} | 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 query_accession
{ my $self = shift;
return $self->{'_query_accession'} = shift if @_;
return $self->{'_query_accession'};} | sub hsp_minscore
{ my $self = shift;
return $self->{'_hsp_minscore'} = shift if @_;
return $self->{'_hsp_minscore'};} | sub algorithm_version
{ my $self = shift;
return $self->{'_algorithm'} = shift if @_;
return $self->{'_algorithm'};
}
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
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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::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)