# # BioStudio functions # =head1 NAME Bio::BioStudio::Analyze::ProteinCodingGenes =head1 VERSION Version 2.10 =head1 DESCRIPTION BioStudio functions =head1 AUTHOR Sarah Richardson <smrichardson@lbl.gov>. =cut package Bio::BioStudio::Analyze::ProteinCodingGenes; require Exporter; use Bio::BioStudio::Mask; use base qw(Exporter); use strict; use warnings; our $VERSION = '2.10'; our @EXPORT_OK = qw( _analyze ); our %EXPORT_TAGS = (BS=> \@EXPORT_OK); my @pcgs = qw(gene mRNA CDS intron five_prime_UTR_intron three_prime_UTR_intron); my @pcgmods = qw(PCR_product tag stop_retained_variant synonymous_codon non_synonymous_codon); =head1 Functions =head2 _analyze() =cut sub _analyze { my ($chromosome, $start, $stop) = @_; my %REPORT; my %FLATS; $start = $start || 1; $stop = $stop || length($chromosome->sequence); my $range = Bio::Range->new(-start => $start, -end => $stop); my @PCGS; my @cdnas; my @genes = $chromosome->db->get_features_by_type('gene'); foreach my $gene (grep { $range->contains($_) } @genes) { my @exons = grep { $_->primary_tag eq 'CDS'} $chromosome->flatten_subfeats($gene); if (scalar @exons) { push @PCGS, $gene; push @cdnas, $chromosome->make_cDNA($gene); } } #Number of protein coding genes { my $key = 'number of protein coding genes'; $FLATS{$key} = scalar(@PCGS); } #Codon Usage { my $key = 'codon usage report'; $FLATS{$key} = $chromosome->GD->generate_codon_report(-sequences => \@cdnas); } my %genehsh = map {$_->id => $_} @PCGS; my %genetags; foreach my $gene (@PCGS) { $genetags{$_}++ foreach ($gene->get_all_tags()); } my %genelengths = map {$_->id => $_->stop - $_->start + 1} @PCGS; my @longgenes = sort {$genelengths{$b->id} <=> $genelengths{$a->id}} @PCGS; #Largest PCG { my $key = 'largest protein coding gene'; my $largestgene = $longgenes[0]; my $note = $genelengths{$largestgene->id} . ' bp'; $REPORT{$key} = [[$largestgene, $note]]; } #Ten largest PCGs { my $key = 'largest protein coding genes'; my @largestgenes = @longgenes[0..9]; $REPORT{$key} = []; foreach my $obj (@largestgenes) { my $note = $genelengths{$obj->id} . ' bp'; push @{$REPORT{$key}}, [$obj, $note]; } } my @shortgenes = reverse @longgenes; #Smallest PCG { my $key = 'smallest protein coding gene'; my $smallestgene = $shortgenes[0]; my $note = $genelengths{$smallestgene->id} . ' bp'; $REPORT{$key} = [[$smallestgene, $note]]; } #Ten smallest PCGs { my $key = 'smallest protein coding genes'; my @smallestgenes = @shortgenes[0..9]; $REPORT{$key} = []; foreach my $obj (@smallestgenes) { my $note = $genelengths{$obj->id} . ' bp'; push @{$REPORT{$key}}, [$obj, $note]; } } if (exists $genetags{orf_classification}) { #Smallest verified PCG { my @vgenes = grep { $_->Tag_orf_classification && $_->Tag_orf_classification ne 'Dubious' } @shortgenes; my $key = 'smallest verified protein coding gene'; my $smallestvgene = $vgenes[0]; my $note = $genelengths{$smallestvgene->id} . ' bp'; $REPORT{$key} = [[$smallestvgene, $note]]; } #Essential PCGs { my @essentials = grep {$_->Tag_essential_status && $_->Tag_essential_status eq 'Essential'} @PCGS; my $key = 'essential protein coding genes'; $REPORT{$key} = []; push @{$REPORT{$key}}, [$_] foreach (@essentials); } #Fastgrowth PCGs { my @fasts = grep {$_->Tag_essential_status && $_->Tag_essential_status eq 'fast_growth'} @PCGS; my $key = 'protein coding genes required for rapid growth'; $REPORT{$key} = []; push @{$REPORT{$key}}, [$_] foreach (@fasts); } } #Genes with introns { my $key = 'protein coding genes with introns'; $REPORT{$key} = []; my @keywords = qw(intron five_prime_UTR_intron three_prime_UTR_intron); my %itypes = map {$_ => 1} @keywords; foreach my $gene (sort {$a->start <=> $b->start} @PCGS) { my @subfeats = $chromosome->flatten_subfeats($gene); my @introns = grep { exists( $itypes{$_->primary_tag} ) } @subfeats; if (scalar(@introns)) { my $number = scalar(@introns) > 1 ? 's' : q{}; my $note = scalar(@introns) . " intron$number"; push @{$REPORT{$key}}, [$gene, $note]; } } } my $genemask = $chromosome->type_mask('CDS'); #Ten largest PCG deserts { my $key = 'largest protein coding gene deserts'; $REPORT{$key} = []; my $deserts = $genemask->find_deserts(); my @ordered = sort {$b->length <=> $a->length} grep {$range->contains($_)} @{$deserts}; foreach my $desert (@ordered[0..9]) { push @{$REPORT{$key}}, [$desert, $desert->length . ' bp']; } } #Overlapping PCGs { my $key = 'protein coding genes overlapping other protein coding genes'; $REPORT{$key} = []; my $olaps = $genemask->find_overlaps(); my @ordered = sort {$b->length <=> $a->length} grep {$range->contains($_)} @{$olaps}; foreach my $olap (@ordered) { my $str = $olap->length . q{ bp }; my @subs = $olap->get_SeqFeatures; $str .= join q{, }, map {$_->display_name} @subs; push @{$REPORT{$key}}, [$olap, $str]; } } return (\%REPORT, \%FLATS); } 1; __END__ =head1 COPYRIGHT AND LICENSE Copyright (c) 2015, BioStudio developers All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * The names of Johns Hopkins, the Joint Genome Institute, the Joint BioEnergy Institute, the Lawrence Berkeley National Laboratory, the Department of Energy, and the BioStudio developers may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. =cut