Bio::Tools::Sim4 Results
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Summary
Bio::Tools::Sim4::Results - Results of one Sim4 run
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Tools::Sim4::Exon
File::Basename
Inherit
Bio::Tools::AnalysisResult
Synopsis
   # to preset the order of EST and genomic file as given on the sim4 
# command line:
my $sim4 = Bio::Tools::Sim4::Results->new(-file => 'result.sim4',
-estfirst => 1);
# to let the order be determined automatically (by length comparison):
$sim4 = Bio::Tools::Sim4::Results->new( -file => 'sim4.results' );
# filehandle:
$sim4 = Bio::Tools::Sim4::Results->new( -fh => \*INPUT );
# parse the results while(my $exonset = $sim4->next_exonset()) { # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Sim4::Exons # as sub features print "Delimited on sequence ", $exonset->seq_id(), "from ", $exonset->start(), " to ", $exonset->end(), "\n"; foreach my $exon ( $exonset->sub_SeqFeature() ) { # $exon is-a Bio::SeqFeature::FeaturePair print "Exon from ", $exon->start, " to ", $exon->end, " on strand ", $exon->strand(), "\n"; # you can get out what it matched using the est_hit attribute my $homol = $exon->est_hit(); print "Matched to sequence ", $homol->seq_id, " at ", $homol->start," to ", $homol->end, "\n"; } } # essential if you gave a filename at initialization (otherwise the file # stays open) $sim4->close();
Description
The sim4 module provides a parser and results object for sim4 output. The
sim4 results are specialised types of SeqFeatures, meaning you can add them
to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner.
The sim4 Exon objects are Bio::SeqFeature::FeaturePair inherited objects. The
$esthit = $exon->est_hit() is the alignment as a feature on the matching
object (normally, an EST), in which the start/end points are where the hit
lies.
To make this module work sensibly you need to run
     sim4 genomic.fasta est.database.fasta
or
sim4 est.fasta genomic.database.fasta
To get the sequence identifiers recorded for the first sequence, too, use
A=4 as output option for sim4.
One fiddle here is that there are only two real possibilities to the matching
criteria: either one sequence needs reversing or not. Because of this, it
is impossible to tell whether the match is in the forward or reverse strand
of the genomic DNA. We solve this here by assuming that the genomic DNA is
always forward. As a consequence, the strand attribute of the matching EST is
unknown, and the strand attribute of the genomic DNA (i.e., the Exon object)
will reflect the direction of the hit.
See the documentation of parse_next_alignment() for abilities of the parser
to deal with the different output format options of sim4.
Methods
_initialize_state
No description
Code
analysis_methodDescriptionCode
parse_next_alignmentDescriptionCode
next_exonsetDescriptionCode
next_featureDescriptionCode
Methods description
analysis_methodcode    nextTop
 Usage     : $sim4->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/sim4/i.
Returns : String
Argument : n/a
parse_next_alignmentcodeprevnextTop
 Title   : parse_next_alignment
Usage : @exons = $sim4_result->parse_next_alignment;
foreach $exon (@exons) {
# do something
}
Function: Parses the next alignment of the Sim4 result file and returns the
found exons as an array of Bio::Tools::Sim4::Exon objects. Call
this method repeatedly until an empty array is returned to get the
results for all alignments.
The $exon->seq_id() attribute will be set to the identifier of the respective sequence for both sequences if A=4 was used in the sim4 run, and otherwise for the second sequence only. If the output does not contain the identifier, the filename stripped of path and extension is used instead. In addition, the full filename will be recorded for both features ($exon inherits off Bio::SeqFeature::SimilarityPair) as tag 'filename'. The length is accessible via the seqlength() attribute of $exon->query() and $exon->est_hit(). Note that this method is capable of dealing with outputs generated with format 0,1,3, and 4 (via the A=n option to sim4). It automatically determines which of the two sequences has been reversed, and adjusts the coordinates for that sequence. It will also detect whether the EST sequence(s) were given as first or as second file to sim4, unless this has been specified at creation time of the object. Example : Returns : An array of Bio::Tools::Sim4::Exon objects Args :
next_exonsetcodeprevnextTop
 Title   : next_exonset
Usage : $exonset = $sim4_result->parse_next_exonset;
print "Exons start at ", $exonset->start(),
"and end at ", $exonset->end(), "\n";
foreach $exon ($exonset->sub_SeqFeature()) {
# do something
}
Function: Parses the next alignment of the Sim4 result file and returns the
set of exons as a container of features. The container is itself
a Bio::SeqFeature::Generic object, with the Bio::Tools::Sim4::Exon
objects as sub features. Start, end, and strand of the container
will represent the total region covered by the exons of this set.
See the documentation of parse_next_alignment() for further reference about parsing and how the information is stored. Example : Returns : An Bio::SeqFeature::Generic object holding Bio::Tools::Sim4::Exon objects as sub features. Args :
next_featurecodeprevnextTop
 Title   : next_feature
Usage : while($exonset = $sim4->next_feature()) {
# do something
}
Function: Does the same as next_exonset(). See there for documentation of
the functionality. Call this method repeatedly until FALSE is
returned.
The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_exonset() at present. Example : Returns : A Bio::SeqFeature::Generic object. Args :
Methods code
_initialize_statedescriptionprevnextTop
sub _initialize_state {
    my($self,@args) = @_;

    # call the inherited method first
my $make = $self->SUPER::_initialize_state(@args); my ($est_is_first) = $self->_rearrange([qw(ESTFIRST)], @args); delete($self->{'_est_is_first'}); $self->{'_est_is_first'} = $est_is_first if(defined($est_is_first)); $self->analysis_method("Sim4");
}
analysis_methoddescriptionprevnextTop
sub analysis_method {
 #-------------
my ($self, $method) = @_; if($method && ($method !~ /sim4/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method);
}
parse_next_alignmentdescriptionprevnextTop
sub parse_next_alignment {
   my ($self) = @_;
   my @exons = ();
   my %seq1props = ();
   my %seq2props = ();
   # we refer to the properties of each seq by reference
my ($estseq, $genomseq, $to_reverse); my $started = 0; my $hit_direction = 1; my $output_fmt = 3; # same as 0 and 1 (we cannot deal with A=2 produced
# output yet)
while(defined($_ = $self->_readline())) { #chomp();
#
# bascially, each sim4 'hit' starts with seq1...
#
/^seq1/ && do { if($started) { $self->_pushback($_); last; } $started = 1; # filename and length of seq 1
/^seq1\s+=\s+(\S+)\,\s+(\d+)/ || $self->throw("Sim4 parsing error on seq1 [$_] line. Sorry!"); $seq1props{'filename'} = $1; $seq1props{'length'} = $2; next; }; /^seq2/ && do { # the second hit has also the database name in the >name syntax
# (in brackets).
/^seq2\s+=\s+(\S+)\s+\(>?(\S+)\s*\)\,\s+(\d+)/|| $self->throw("Sim4 parsing error on seq2 [$_] line. Sorry!"); $seq2props{'filename'} = $1; $seq2props{'seqname'} = $2; $seq2props{'length'} = $3; next; }; if(/^>(\S+)\s*(.*)$/) { # output option was A=4, which not only gives the complete
# description lines, but also causes the longer sequence to be
# reversed if the second file contained one (genomic) sequence
$seq1props{'seqname'} = $1; $seq1props{'description'} = $2 if $2; $output_fmt = 4; # we handle seq1 and seq2 both here
if(defined($_ = $self->_readline()) && (/^>(\S+)\s*(.*)$/)) { $seq2props{'seqname'} = $1; # redundant, since already set above
$seq2props{'description'} = $2 if $2; } next; } /^\(complement\)/ && do { $hit_direction = -1; next; }; # this matches
# start-end (start-end) pctid%
if(/(\d+)-(\d+)\s+\((\d+)-(\d+)\)\s+(\d+)%/) { $seq1props{'start'} = $1; $seq1props{'end'} = $2; $seq2props{'start'} = $3; $seq2props{'end'} = $4; my $pctid = $5; if(! defined($estseq)) { # for the first time here: need to set the references referring
# to seq1 and seq2
if(! exists($self->{'_est_is_first'})) { # detect which one is the EST by looking at the lengths,
# and assume that this holds throughout the entire result
# file (i.e., when this method is called for the next
# alignment, this will not be checked again)
if($seq1props{'length'} > $seq2props{'length'}) { $self->{'_est_is_first'} = 0; } else { $self->{'_est_is_first'} = 1; } } if($self->{'_est_is_first'}) { $estseq =\% seq1props; $genomseq =\% seq2props; # if the EST is given first, A=4 selects the genomic
# seq for being reversed (reversing the EST is default)
$to_reverse = ($output_fmt == 4) ? $genomseq : $estseq; } else { $estseq =\% seq2props; $genomseq =\% seq1props; # if the EST is the second, A=4 does not change the
# seq being reversed (always the EST is reversed)
$to_reverse = $estseq; } } if($hit_direction == -1) { # we have to reverse the coordinates of one of both seqs
my $tmp = $to_reverse->{'start'}; $to_reverse->{'start'} = $to_reverse->{'length'} - $to_reverse->{'end'} + 1; $to_reverse->{'end'} = $to_reverse->{'length'} - $tmp + 1; } # create and initialize the exon object
my $exon = Bio::Tools::Sim4::Exon->new( '-start' => $genomseq->{'start'}, '-end' => $genomseq->{'end'}, '-strand' => $hit_direction); if(exists($genomseq->{'seqname'})) { $exon->seq_id($genomseq->{'seqname'}); } else { # take filename stripped of path as fall back
my ($basename) = &File::Basename::fileparse($genomseq->{'filename'}, '\..*'); $exon->seq_id($basename); } $exon->feature1()->add_tag_value('filename', $genomseq->{'filename'}); # feature1 is supposed to be initialized to a Similarity object,
# but we provide a safety net
if($exon->feature1()->can('seqlength')) { $exon->feature1()->seqlength($genomseq->{'length'}); } else { $exon->feature1()->add_tag_value('SeqLength', $genomseq->{'length'}); } # create and initialize the feature wrapping the 'hit' (the EST)
my $fea2 = Bio::SeqFeature::Similarity->new( '-start' => $estseq->{'start'}, '-end' => $estseq->{'end'}, '-strand' => 0, '-primary' => "aligning_EST"); if(exists($estseq->{'seqname'})) { $fea2->seq_id($estseq->{'seqname'}); } else { # take filename stripped of path as fall back
my ($basename) = &File::Basename::fileparse($estseq->{'filename'}, '\..*'); $fea2->seq_id($basename); } $fea2->add_tag_value('filename', $estseq->{'filename'}); $fea2->seqlength($estseq->{'length'}); # store
$exon->est_hit($fea2); # general properties
$exon->source_tag($self->analysis_method()); $exon->percentage_id($pctid); $exon->score($exon->percentage_id()); # push onto array
push(@exons, $exon); next; # back to while loop
} } return @exons;
}
next_exonsetdescriptionprevnextTop
sub next_exonset {
    my $self = shift;
    my $exonset;

    # get the next array of exons
my @exons = $self->parse_next_alignment(); unless( @exons ) { return if eof($self->_fh); return $self->next_exonset; } # create the container of exons as a feature object itself, with the
# data of the first exon for initialization
$exonset = Bio::SeqFeature::Generic->new('-start' => $exons[0]->start(), '-end' => $exons[0]->end(), '-strand' => $exons[0]->strand(), '-primary' => "ExonSet"); $exonset->source_tag($exons[0]->source_tag()); $exonset->seq_id($exons[0]->seq_id()); # now add all exons as sub features, with enabling EXPANsion of the region
# covered in total
foreach my $exon (@exons) { $exonset->add_sub_SeqFeature($exon, 'EXPAND'); } return $exonset;
}
next_featuredescriptionprevnextTop
sub next_feature {
    my ($self,@args) = @_;
    # even though next_exonset doesn't expect any args (and this method
# does neither), we pass on args in order to be prepared if this changes
# ever
return $self->next_exonset(@args); } 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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney, Hilmar LappTop
Ewan Birney <birney-at-sanger.ac.uk>
Hilmar Lapp <hlapp-at-gmx.net> or <hilmar.lapp-at-pharma.novartis.com>.
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _