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adding back Est2Genome.pm -DOH

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commit 7dd1acaf513187ab78fef1b052012544da5fca75 1 parent 96fcec1
@majensen majensen authored
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  1. +360 −0 Bio/Tools/Run/Est2Genome.pm
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360 Bio/Tools/Run/Est2Genome.pm
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+#
+# BioPerl module for Bio::Tools::Est2Genome
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Cared for by Jason Stajich <jason-at-bioperl.org>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Est2Genome - Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
+
+=head1 SYNOPSIS
+
+ use Bio::Tools::Est2Genome;
+
+ my $featureiter = Bio::Tools::Est2Genome->new(-file => 'output.est2genome');
+
+ # This is going to be fixed to use the SeqAnalysisI next_feature
+ # Method eventually when we have the objects to put the data in
+ # properly
+ while( my $f = $featureiter->parse_next_gene ) {
+ # process Bio::SeqFeature::Generic objects here
+ }
+
+=head1 DESCRIPTION
+
+This module is a parser for C<est2genome> [EMBOSS] alignments of est/cdna
+sequence to genomic DNA. This is generally accepted as the best
+program for predicting splice sites based on est/dnas (as far as I know).
+
+This module currently does not try pull out the ungapped alignments
+(Segment) but may in the future.
+
+=head1 FEEDBACK
+
+=head2 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
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<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.
+
+=head2 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 the
+web:
+
+ https://github.com/bioperl/bioperl-live/issues
+
+=head1 AUTHOR - Jason Stajich
+
+Email jason-at-bioperl.org
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Tools::Est2Genome;
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::Root::Root;
+use Bio::SeqFeature::Gene::Exon;
+use Bio::SeqFeature::Gene::Transcript;
+use Bio::SeqFeature::Gene::Intron;
+use Bio::SeqFeature::Gene::GeneStructure;
+use Bio::SeqFeature::SimilarityPair;
+
+use base qw(Bio::Tools::AnalysisResult);
+
+=head2 new
+
+ Title : new
+ Usage : my $obj = Bio::Tools::Est2Genome->new();
+ Function: Builds a new Bio::Tools::Est2Genome object
+ Returns : an instance of Bio::Tools::Est2Genome
+ Args : -file => 'output.est2genome' or
+ -fh => \*EST2GENOMEOUTPUT
+ -genomefirst => 1 # genome was the first input (not standard)
+
+=cut
+
+sub _initialize_state {
+ my($self,@args) = @_;
+
+ # call the inherited method first
+ my $make = $self->SUPER::_initialize_state(@args);
+
+ my ($genome_is_first) = $self->_rearrange([qw(GENOMEFIRST)], @args);
+
+ delete($self->{'_genome_is_first'});
+ $self->{'_genome_is_first'} = $genome_is_first if(defined($genome_is_first));
+ $self->analysis_method("est2genome");
+}
+
+=head2 analysis_method
+
+ Usage : $sim4->analysis_method();
+ Purpose : Inherited method. Overridden to ensure that the name matches
+ /est2genome/i.
+ Returns : String
+ Argument : n/a
+
+=cut
+
+#-------------
+sub analysis_method {
+#-------------
+ my ($self, $method) = @_;
+ if($method && ($method !~ /est2genome/i)) {
+ $self->throw("method $method not supported in " . ref($self));
+ }
+ return $self->SUPER::analysis_method($method);
+}
+
+=head2 parse_next_gene
+
+ Title : parse_next_gene
+ Usage : @gene = $est2genome_result->parse_next_gene;
+ foreach $exon (@exons) {
+ # do something
+ }
+
+ Function: Parses the next alignments of the est2genome result file and
+ returns the found exons as an array of
+ Bio::SeqFeature::SimilarityPair 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.
+ The length is accessible via the seqlength()
+ attribute of $exon->query() and
+ $exon->est_hit().
+ Returns : An array (or array reference) of Bio::SeqFeature::SimilarityPair and Bio::SeqFeature::Generic objects
+ or Bio::SeqFeature::Gene::GeneStructure
+ Args : flag(1/0) indicating to return Bio::SeqFeature::Gene::GeneStructure or Bio::SeqFeature::SimilarityPair
+ defaults to 0
+
+=cut
+
+sub parse_next_gene {
+ my ($self,$return_gene) = @_;
+ return $self->_parse_gene_struct if $return_gene;
+ my $seensegment = 0;
+ my @features;
+ my ($qstrand,$hstrand) = (1,1);
+ my $lasthseqname;
+ while( defined($_ = $self->_readline) ) {
+ if( /Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) {
+ if( $seensegment ) {
+ $self->_pushback($_);
+ return wantarray ? @features : \@features;
+ }
+ $hstrand = -1 if $1 eq 'reversed';
+ $qstrand = -1 if $4 eq 'REVERSED GENE';
+ #$self->debug( "1=$1, 2=$2, 4=$4\n");
+ }
+ elsif( /^Exon/ ) {
+ my ($name,$score,$perc_ident,$qstart,$qend,$qseqname,
+ $hstart,$hend, $hseqname) = split;
+ $lasthseqname = $hseqname;
+ my $query = Bio::SeqFeature::Similarity->new(-primary => $name,
+ -source => $self->analysis_method,
+ -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE
+ -start => $qstart,
+ -end => $qend,
+ -strand => $qstrand,
+ -score => $score,
+ -tag => {
+# 'Location' => "$hstart..$hend",
+ 'Sequence' => "$hseqname",
+ 'identity' => $perc_ident,
+ }
+ );
+ my $hit = Bio::SeqFeature::Similarity->new(-primary => 'exon_hit',
+ -source => $self->analysis_method,
+ -seq_id => $hseqname,
+ -start => $hstart,
+ -end => $hend,
+ -strand => $hstrand,
+ -score => $score,
+ -tag => {
+# 'Location' => "$qstart..$qend",
+ 'Sequence' => "$qseqname",
+ 'identity' => $perc_ident,
+ }
+ );
+ push @features, Bio::SeqFeature::SimilarityPair->new
+ (-query => $query,
+ -hit => $hit,
+ -source => $self->analysis_method);
+ } elsif( /^([\-\+\?])(Intron)/) {
+ my ($name,$score,$perc_ident,$qstart,$qend,$qseqname) = split;
+ push @features, Bio::SeqFeature::Generic->new(-primary => $2,
+ -source => $self->analysis_method,
+ -start => $qstart,
+ -end => $qend,
+ -strand => $qstrand,
+ -score => $score,
+ -seq_id => $qseqname,
+ -tag => {
+ 'identity' => $perc_ident,
+ 'Sequence' => $lasthseqname});
+ } elsif( /^Span/ ) {
+ } elsif( /^Segment/ ) {
+ $seensegment = 1;
+ } elsif( /^\s+$/ ) { # do nothing
+ } else {
+ $self->warn( "unknown line $_\n");
+ }
+ }
+ return unless( @features );
+ return wantarray ? @features : \@features;
+}
+
+sub _parse_gene_struct {
+ my ($self) = @_;
+ my $seensegment = 0;
+ my @features;
+ my ($qstrand,$hstrand) = (1,1);
+ my $lasthseqname;
+ my $gene = Bio::SeqFeature::Gene::GeneStructure->new(-source => $self->analysis_method);
+ my $transcript = Bio::SeqFeature::Gene::Transcript->new(-source => $self->analysis_method);
+ my @suppf;
+ my @exon;
+ while( defined($_ = $self->_readline) ) {
+ if( /Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) {
+ if( $seensegment ) {
+ $self->_pushback($_);
+ return $gene;
+ }
+ $hstrand = -1 if $1 eq 'reversed';
+ $qstrand = -1 if $4 eq 'REVERSED GENE';
+ }
+ elsif( /^Exon/ ) {
+ my ($name,$score,$perc_ident,$qstart,$qend,$qseqname,$hstart,$hend, $hseqname) = split;
+ $lasthseqname = $hseqname;
+ my $exon = Bio::SeqFeature::Gene::Exon->new(-primary => $name,
+ -source => $self->analysis_method,
+ -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE
+ -start => $qstart,
+ -end => $qend,
+ -strand => $qstrand,
+ -score => $score,
+ -tag => {
+ #'Location' => "$hstart..$hend",
+ 'identity' => $perc_ident,
+ 'Sequence' => "$hseqname",
+ }
+ );
+ $transcript->seq_id($qseqname) unless $transcript->seq_id;
+ $exon->add_tag_value('phase',0);
+ push @exon, $exon;
+
+ } elsif( /^([\-\+\?])(Intron)/) {
+ next; #intron auto matically built from exons..hope thats ok..
+ } elsif( /^Span/ ) {
+ } elsif( /^Segment/ ) {
+ my ($name,$score,$perc_ident,$qstart,$qend,$qseqname,$hstart,$hend, $hseqname) = split;
+ my $query = Bio::SeqFeature::Similarity->new(-primary => $name,
+ -source => $self->analysis_method,
+ -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE
+ -start => $qstart,
+ -end => $qend,
+ -strand => $qstrand,
+ -score => $score,
+ -tag => {
+# 'Location' => "$hstart..$hend",
+ 'Sequence' => "$hseqname",
+ 'identity' => $perc_ident,
+ }
+ );
+ my $hit = Bio::SeqFeature::Similarity->new(-primary => 'exon_hit',
+ -source => $self->analysis_method,
+ -seq_id => $hseqname,
+ -start => $hstart,
+ -end => $hend,
+ -strand => $hstrand,
+ -score => $score,
+ -tag => {
+ # 'Location' => "$qstart..$qend",
+ 'Sequence' => "$qseqname",
+ 'identity' => $perc_ident,
+ }
+ );
+ my $support = Bio::SeqFeature::SimilarityPair->new(-query => $query,
+ -hit => $hit,
+ -source => $self->analysis_method);
+ push @suppf, $support;
+ } elsif( /^\s+$/ ) { # do nothing
+ } else {
+ $self->warn( "unknown line $_\n");
+ }
+ }
+ return unless $#exon >=0;
+ foreach my $e(@exon){
+ my @add;
+ foreach my $sf(@suppf){
+ if($sf->overlaps($e)){
+ push @add,$sf;
+ }
+ }
+ $e->add_tag_value('supporting_feature',@add);
+ $transcript->add_exon($e);
+ }
+
+ $gene->add_transcript($transcript);
+ $gene->seq_id($transcript->seq_id);
+ return $gene;
+}
+
+=head2 next_feature
+
+ Title : next_feature
+ Usage : $seqfeature = $obj->next_feature();
+ Function: Returns the next feature available in the analysis result, or
+ undef if there are no more features.
+ Example :
+ Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
+ more features.
+ Args : none
+
+=cut
+
+sub next_feature {
+ my ($self) = shift;
+ $self->throw("We haven't really done this right, yet, use parse_next_gene");
+}
+
+
+1;

6 comments on commit 7dd1aca

@majensen
Collaborator

Well, this obviously killed the blame; would be grateful if a real git person could repair...sorry

@tsibley

The previous blame is still available, but you have to ask git to annotate two revisions before this one. Lots of tools let you follow the chain of parent commits back while blaming. Repairing isn't possible without rewriting history, which would be worse than letting mistakes be.

@majensen
Collaborator
@fjossandon
Collaborator

Mark, you added it back in the wrong location. Est2Genome.pm was located in the "Bio/Tools" folder, not in "Bio/Tools/Run", so now "t/Tools/Est2Genome.t" can't find the module to compile and fails. Could you please move it back to its original location??

@majensen
Collaborator
@fjossandon
Collaborator

Thanks Mark!!! :+1:

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