Bio::SearchIO::erpin - SearchIO-based ERPIN parser
Index
Code Index:
NAME
Bio::SearchIO::erpin - SearchIO-based ERPIN parser
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.
FEEDBACK
Mailing Lists
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
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 Bugs
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 Fields
Email cjfields-at-uiuc-dot-edu
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
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)
next_result
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_element
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_element
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'
element
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_hash
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
characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
within_element
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_element
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_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
result_count
Title : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
query_accession
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_minscore
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_version
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)
#
# BioPerl module for Bio::SearchIO::erpin
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields <cjfields-at-uiuc-dot-edu>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
# Let the code begin...
package Bio::SearchIO::erpin;
use strict;
use Data::Dumper;
use base qw(Bio::SearchIO);
my %MODEMAP = (
'Result' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
my %MAPPING = (
'Hsp_bit-score' => 'HSP-bits',
'Hsp_score' => 'HSP-score',
'Hsp_evalue' => 'HSP-evalue', # no evalues yet
'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',
# not supported yet
'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', # none yet
'Hit_score' => 'HIT-score', # best HSP bit score
'Hit_bits' => 'HIT-bits', # best HSP bit score
'ERPIN_program' => 'RESULT-algorithm_name', # get/set
'ERPIN_version' => 'RESULT-algorithm_version', # get/set
'ERPIN_query-def'=> 'RESULT-query_name', # get/set
'ERPIN_query-len'=> 'RESULT-query_length',
'ERPIN_query-acc'=> 'RESULT-query_accession', # get/set
'ERPIN_querydesc'=> 'RESULT-query_description', # get/set
'ERPIN_db' => 'RESULT-database_name', # get/set
'ERPIN_db-len' => 'RESULT-database_entries', # none yet
'ERPIN_db-let' => 'RESULT-database_letters', # none yet
'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' },
);
my $MINSCORE = 0;
my $DEFAULT_VERSION = '4.2.5';
my $DEFAULT_ALGORITHM = 'erpin';
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; # 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();
}
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;
}
}
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;
}
sub element {
my ( $self, $data ) = @_;
# simple data calls (%MAPPING) do not need start_element
$self->characters($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;