Bio::Tools::Spidey Results
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Summary
Bio::Tools::Spidey::Results - Results of a Spidey run
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Tools::Spidey::Exon
File::Basename
Inherit
Bio::Tools::AnalysisResult
Synopsis
   use Bio::Tools::Spidey::Results;
my $spidey = Bio::Tools::Spidey::Results->new(-file => 'result.spidey' );
# or my $spidey = Bio::Tools::Spidey::Results->new( -fh => \*INPUT ); # get the exons before doing anything else my $exonset = $spidey->next_exonset(); # parse the results my @exons = $exonset->sub_SeqFeature(); print "Total no of Exons: ", scalar(@exons), "\n"; print "Genomic sequence length: ", $spidey->genomic_dna_length(), "\n"; # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Spidey::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) $spidey->close();
Description
The spidey module provides a parser and results object for spidey
output. The spidey results are specialised types of SeqFeatures,
meaning you can add them to AnnSeq objects fine, and manipulate them
in the "normal" seqfeature manner.
The spidey Exon objects are Bio::SeqFeature::FeaturePair inherited
objects. The $esthit = $exon->est_hit() is the alignment as a
feature on the matching object (normally, a cDNA), in which the
start/end points are where the hit lies.
To make this module work sensibly you need to run
     spidey -i genomic.fasta -m cDNA.fasta
Methods
_initialize_state
No description
Code
analysis_methodDescriptionCode
parse_next_alignmentDescriptionCode
next_exonsetDescriptionCode
next_featureDescriptionCode
genomic_dna_lengthDescriptionCode
splicesitesDescriptionCode
est_coverageDescriptionCode
overall_percentage_idDescriptionCode
missing_mrna_endsDescriptionCode
Methods description
analysis_methodcode    nextTop
 Usage     : $spidey->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/Spidey/i.
Returns : String
Argument : n/a
parse_next_alignmentcodeprevnextTop
 Title   : parse_next_alignment
Usage : @exons = $spidey_result->parse_next_alignment;
foreach $exon (@exons) {
# do something
}
Function: Parses the next alignment of the Spidey result file and returns the
found exons as an array of Bio::Tools::Spidey::Exon objects. Call
this method repeatedly until an empty array is returned to get the
results for all alignments.
Example :
Returns : An array of Bio::Tools::Spidey::Exon objects
Args :
next_exonsetcodeprevnextTop
  Title   : next_exonset
Usage : $exonset = $spidey_result->parse_next_exonset;
print "Exons start at ", $exonset->start(),
"and end at ", $exonset->end(), "\n";
for $exon ($exonset->sub_SeqFeature()) {
# do something
}
Function: Parses the next alignment of the Spidey 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::Spidey::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::Spidey::Exon objects as sub features. Args :
next_featurecodeprevnextTop
  Title   : next_feature
Usage : while($exonset = $spidey->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 :
genomic_dna_lengthcodeprevnextTop
    Title   : genomic_dna_length
Usage : $spidey->genomic_dna_length();
Function: Returns the length of the genomic DNA used in this Spidey result
Example :
Returns : An integer value.
Args :
splicesitescodeprevnextTop
    Title   : splicesites
Usage : $spidey->splicesites();
Function: Returns the number of splice sites found in this Spidey result
Example :
Returns : An integer value.
Args :
est_coveragecodeprevnextTop
    Title   : est_coverage
Usage : $spidey->est_coverage();
Function: Returns the percent of est coverage in this Spidey result
Example :
Returns : An integer value.
Args :
overall_percentage_idcodeprevnextTop
    Title   : overall_percentage_id
Usage : $spidey->overall_percentage_id();
Function: Returns the overall percent id in this Spidey result
Example :
Returns : An float value.
Args :
missing_mrna_endscodeprevnextTop
    Title   : missing_mrna_ends
Usage : $spidey->missing_mrna_ends();
Function: Returns left/right/neither from Spidey
Example :
Returns : A string value.
Args :
Methods code
_initialize_statedescriptionprevnextTop
sub _initialize_state {
    my($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));
$self->analysis_method("Spidey");
}
analysis_methoddescriptionprevnextTop
sub analysis_method {
 #-------------
my ($self, $method) = @_; if($method && ($method !~ /Spidey/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method);
}
parse_next_alignmentdescriptionprevnextTop
sub parse_next_alignment {
    my ($self) = @_;
    # for strand 1 = plus, -1 = minus
my ($started,$version,$strand, $exoncount) = (0,0,0,-1); my (%seq1props,%seq2props,@exons); # we refer to the properties of each seq by reference
while(defined($_ = $self->_readline())) { chomp; #
# bascially, parse a Spidey result...
#
# matches: --SPIDEY version 1.40--
if( /^--SPIDEY\s+version\s+(\d+\.\d+)--/) { if($started) { $self->_pushback($_); return\@ exons; } $version = $1; if ($version != 1.40) { $self->throw("Spidey parser only designed to work with Spidey v1.40\n"); } $started = 1; } elsif (/^Genomic:\s+(\S+)\s.*,\s+(\d+)\sbp$/ ) { # matches: Genomic: lcl|some_name other information, 1234 bp
# $seq1props{'filename'} = $1;
$seq1props{'seqname'} = $1; $seq1props{'length'} = $2; $self->genomic_dna_length($seq1props{'length'}); } elsif( /^mRNA:\s+(\S+)\s.*,(?:\s+mRNA\s+sequence,)?\s(\d+)\sbp$/ ) { # matches: mRNA:
# $seq2props{'filename'} = $1;
$seq2props{'seqname'} = $1; $seq2props{'length'} = $2; } elsif( /^Strand:/ ) { if (/plus/) { $strand = 1; } else { $strand = -1; } } elsif( /^Number of exons: (\d+)/ ) { $exoncount = $1; my ($genomic_start, $genomic_stop, $cdna_start, $cdna_stop, $id, $mismatches, $gaps, $splice_donor, $splice_acceptor, $uncertain); # the next $exoncount lines contains information
# about the matches of each exon. we should parse
# this information here
for (my $ec = 1; $ec <= $exoncount; $ec++) { if (defined($_ = $self->_readline())) { chomp; if (/^Exon\s$ec[\(\)-]*:\s(\d+)-(\d+)\s\(gen\)\s+(\d+)-(\d+)\s\(mRNA\)\s+id\s([\d\.inf-]+)%\s+mismatches\s(\d+)\s+gaps\s(\d+)\s+splice\ssite\s\(d\s+a\):\s(\d+)\s+(\d+)\s*(\w*)/) { $genomic_start = $1; $genomic_stop = $2; $cdna_start = $3; $cdna_stop = $4; $id = $5; $mismatches = $6; $gaps = $7; $splice_donor = $8; $splice_acceptor = $9; $uncertain = $10; } else { $self->throw( "Failed to match anything:\n$_\n"); } my $exon = Bio::Tools::Spidey::Exon->new (-start => $genomic_start, -end => $genomic_stop, -strand => $strand); $exon->seq_id($seq1props{'seqname'}); # feature1 is supposed to be initialized to a Similarity object, but we provide a safety net
if ($exon->feature1->can('seqlength')) { $exon->feature1->seqlength($seq1props{'length'}); } else { $exon->feature1->add_tag_value('seqlength', $seq1props{'length'}); } # create and initialize the feature wrapping the 'hit' (the cDNA)
my $fea2 = Bio::SeqFeature::Similarity->new (-start => $cdna_start, -end => $cdna_stop, -strand => $strand, -seq_id => $seq2props{'seqname'}, -primary => "aligning_cDNA"); $fea2->seqlength($seq2props{'length'}); # store
$exon->est_hit($fea2); # general properties
$exon->source_tag($self->analysis_method()); $exon->percentage_id($5); $exon->mismatches($6); $exon->gaps($7); $exon->donor($8); $exon->acceptor($9); # push onto array
push(@exons, $exon); } else { $self->throw("Unexpected end of file reached\n"); } } } elsif( /^Number of splice sites:\s+(\d+)/ ) { $self->splicesites($1); } elsif( /^mRNA coverage:\s+(\d+)%/ ) { $self->est_coverage($1); } elsif(/^overall percent identity:\s+([\d\.]+)%/ ) { $self->overall_percentage_id($1); } elsif(/^Missing mRNA ends:\s+(\w+)/ ) { $self->missing_mrna_ends($1); } elsif( /^Exon (\d+): (\d+)-(\d+) \(gen\)\s+(\d+)-(\d+) \(mRNA\)/ ) { my ($exon_num, $gen_start, $gen_stop, $cdna_start, $cdna_stop); $exon_num = $1; $gen_start = $2; $gen_stop = $3; $cdna_start = $4; $cdna_stop = $5; } elsif( /No alignment found/ ) { return []; } else { #$self->debug("unmatched $_\n");
} } # Typical format:
# Exon 1: 36375798-36375691 (gen) 1-108 (mRNA)
#
#
# CCTCTTTTTCTTTGCAGGGTATATACCCAGTTACTTAGACAAGGATGAGCTATGTGTAGT
# | ||||||||||||||||||||||||||||||||||||||||||||||
# ATGTCAGGGTATATACCCAGTTACTTAGACAAGGATGAGCTATGTGTAGT
# M S G Y I P S Y L D K D E L C V V
#
#
# ATGTGGGGACAAAGCCACCGGATATCATTATCGCTGCATCACTTGTGAAGGTTGCAAGGT
# ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
# ATGTGGGGACAAAGCCACCGGATATCATTATCGCTGCATCACTTGTGAAGGTTGCAAG
# C G D K A T G Y H Y R C I T C E G C K
#
#
# AAATGGCA
#
@exons ? return\@ exons : return ;
}
next_exonsetdescriptionprevnextTop
sub next_exonset {
    my $self = shift;
    my $exonset;

    # get the next array of exons
my $exons = $self->parse_next_alignment(); if( ! defined $exons ) { $self->warn("No exons returned"); return; } if( @$exons == 0 ) { return Bio::SeqFeature::Generic->new(); } # 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->[-1]->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 $self->next_exonset(@args);
}
genomic_dna_lengthdescriptionprevnextTop
sub genomic_dna_length {
    my ($self, @args) = @_;
    my $val;

    if(@args) {
	$val = shift(@args);
	$self->{'genomic_dna_length'} = $val;
    } else {
	$val = $self->{'genomic_dna_length'};
    }
    return $val;
}
splicesitesdescriptionprevnextTop
sub splicesites {
    my ($self, @args) = @_;
    my $val;

    if(@args) {
	$val = shift(@args);
	$self->{'splicesites'} = $val;
    } else {
	$val = $self->{'splicesites'};
    }
    return $val;
}
est_coveragedescriptionprevnextTop
sub est_coverage {
     my ($self, @args) = @_;
     my $val;
     
     if(@args) {
	 $val = shift(@args);
	 $self->{'est_coverage'} = $val;
     } else {
	 $val = $self->{'est_coverage'};
     }
     return $val;
}
overall_percentage_iddescriptionprevnextTop
sub overall_percentage_id {
    my ($self, @args) = @_;
    my $val;

    if(@args) {
	$val = shift(@args);
	$self->{'overall_percentage_id'} = $val;
    } else {
	$val = $self->{'overall_percentage_id'};
    }
    return $val;
}
missing_mrna_endsdescriptionprevnextTop
sub missing_mrna_ends {
    my ($self, @args) = @_;
    my $val;

    if(@args) {
	$val = shift(@args);
	$self->{'missing_mrna_ends'} = $val;
    } else {
	$val = $self->{'missing_mrna_ends'};
    }
    return $val;
}

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 - Ryan GolharTop
Email golharam@umdnj.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _