test select best transcript , complete gtf to se , clean utrs

conf/LoggerConfig.pm

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+package conf::LoggerConfig;
+
+use strict;
+use warnings;
+
+use Log::Log4perl;
+
+Log::Log4perl->init(\<<'EOT');
+    log4perl.rootLogger = DEBUG, LOGFILE, SCREEN
+    log4perl.appender.Screen = Log::Log4perl::Appender::Screen
+    log4perl.appender.SCREEN.stderr = 1
+    log4perl.appender.Screen.layout = Log::Log4perl::Layout::SimpleLayout
+    log4perl.appender.File = Log::Log4perl::Appender::File
+    log4perl.appender.File.filename = /path/to/your/logfile.log
+    log4perl.appender.File.layout = Log::Log4perl::Layout::PatternLayout
+    log4perl.appender.File.layout.ConversionPattern = %d %p %m %n
+
+EOT
+
+our $logger = Log::Log4perl->get_logger();
+
+1;

src/perl/ensembl/tools/anno/support_scripts_perl/Utils.pm

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+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#      http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+=head1 NAME
+
+Src::Perl::EnsEMBL::Tools::Anno::Support_scripts_perl::Utils - utilities for genset finalisation 
+
+=head1 SYNOPSIS
+
+  use Src::Perl::EnsEMBL::Tools::Anno::Support_scripts_perl::Utils  qw(sub);
+
+  or 
+
+  use Src::Perl::EnsEMBL::Tools::Anno::Support_scripts_perl::Utils 
+
+  to get all methods
+
+=head1 DESCRIPTION
+
+=cut
+
+
+package Src::Perl::EnsEMBL::Tools::Anno::Support_scripts_perl::Utils; #or just Utils??
+#Make sure that the MyUtils.pm module is in the same directory or is in a directory included in your Perl library path (@INC).
+use strict;
+use warnings;
+use feature 'say';
+use Exporter;
+
+use Bio::EnsEMBL::Utils::Exception qw(warning throw);
+use Bio::EnsEMBL::Gene;
+use Bio::EnsEMBL::Exon;
+use Bio::EnsEMBL::Transcript;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::Translation;
+use Bio::EnsEMBL::Analysis::Runnable::GeneBuilder;
+use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::GeneUtils;
+use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils qw(calculate_exon_phases features_overlap clone_Transcript);
+use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranslationUtils qw(compute_translation);
+use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonUtils qw(clone_Exon);
+use Bio::EnsEMBL::Variation::Utils::FastaSequence qw(setup_fasta);
+use Getopt::Long qw(:config no_ignore_case);
+
+use vars qw (@ISA @EXPORT);
+
+@ISA = qw(Exporter);
+@EXPORT = qw(
+  check_gtf_file
+  setup_fasta
+  set_slice  
+  create_analysis_object        
+  set_transcript
+  set_exon
+  set_translation
+  set_canonical_transcript
+  parse_region_details
+  set_attributes
+  build_translation
+            );
+
+
+
+=head2 check_gtf_file
+
+Validate GTF file.
+
+=cut
+
+sub check_gtf_file {
+    my ($gtf_file) = @_;
+    die "Could not open the GTF file, path used: $gtf_file" unless -e $gtf_file;
+}
+
+=head2 setup_fasta
+
+Set up fasta file
+
+=cut
+sub setup_fasta {
+    my $genome_file = @_;
+
+    if ($genome_file && -e $genome_file) {
+        setup_fasta(-FASTA => $genome_file);
+    }
+
+}
+
+
+=head2 set_slice
+
+Define slice object.
+
+=cut
+sub set_slice {
+    my ($region_name, $region_start, $region_end, $strand) = @_;
+    my $region_length = $region_end - $region_start + 1;
+    my $slice = Bio::EnsEMBL::Slice->new(
+        -start             => $region_start,
+        -end               => $region_end,
+        -strand            => $strand,
+        -seq_region_name   => $region_name,
+        -seq_region_length => $region_length
+    );
+    return $slice;
+}
+
+=head2 create_analysis_object
+
+Define analysis object.
+
+=cut
+sub create_analysis_object {
+    my ($analysis_name, $module_name) = @_;
+
+    my $analysis = Bio::EnsEMBL::Analysis->new(
+        -logic_name => $analysis_name,
+        -module     => $module_name
+    );
+
+    return $analysis;
+}
+
+=head2 set_transcript
+
+Define transcript object.
+
+=cut
+sub set_transcript {
+    my ($exons, $transcript_id, $biotype, $slice) = @_;
+    my $transcript = Bio::EnsEMBL::Transcript->new(-EXONS => $exons);
+    $transcript->stable_id($transcript_id);
+    $transcript->biotype($biotype);
+    $transcript->slice($slice);
+    return $transcript;
+}
+
+=head2 set_exon
+
+Define exon object.
+
+=cut
+sub set_exon {
+    my ($start, $end, $strand, $slice) = @_;
+    my $exon = Bio::EnsEMBL::Exon->new(
+        -START     => $start,
+        -END       => $end,
+        -STRAND    => $strand,
+        -SLICE     => $slice,
+        -PHASE     => -1,
+        -END_PHASE => -1);
+    return $exon;
+}
+
+=head2 set_translation
+
+Define transcript object.
+
+=cut
+sub set_translation {
+    my ($start_exon, $end_exon) = @_;
+    my $translation = Bio::EnsEMBL::Translation->new();
+    $translation->start_Exon($start_exon);
+    $translation->start(1);
+    $translation->end_Exon($end_exon);
+    $translation->end($end_exon->length());
+    return $translation;
+}
+
+
+=head2 set_canonical_transcript
+
+        # This array will store exactly what to write. By default, we would write the gene as constructed to this point.
+        # However, if the run is just to process a particular type of transcripts into a cleaned set, we may want to
+        # pull those back out into single transcript genes for further processing later. In that case, the array will
+        # be replaced with single transcript genes
+
+=cut
+
+sub set_canonical_transcript {
+    my ($gene) = @_;
+
+    my $transcripts = $gene->get_all_Transcripts();
+    my $current_canonical = pop(@$transcripts);
+
+    # Iterate through each transcript and set the canonical transcript based on certain criteria
+    foreach my $transcript (@$transcripts) {
+        my $current_translation = $current_canonical->translation();
+        my $new_translation = $transcript->translation();
+
+        if (!$current_translation || ($current_translation->length() < $new_translation->length()) ||
+            ($current_translation->length() == $new_translation->length() && $current_canonical->length() < $transcript->length()) ||
+            !($current_canonical->translation()) && $current_canonical->length() < $transcript->length()) {
+            $current_canonical = $transcript;
+        }
+    }
+
+    # Set the canonical transcript for the gene
+    $gene->canonical_transcript($current_canonical);
+    return $gene;
+}
+
+=head2 set_attributes
+
+Get attributes.
+
+=cut
+
+sub set_attributes {
+    my ($attribute_string) = @_;
+    my $attribute_pairs = {};
+
+    my @attribute_array = split(";",$attribute_string);
+    foreach my $attribute (@attribute_array) {
+        my @pairs = split(" ",$attribute);
+        if(scalar(@pairs) == 2) {
+        $pairs[1] =~ s/\"//g;
+        $attribute_pairs->{$pairs[0]} = $pairs[1];
+        } else {
+        $attribute =~ s/ //g;
+        $attribute_pairs->{$attribute} = 1;
+        }
+    }
+
+    return($attribute_pairs);
+}
+=head2 parse_region_details
+
+Parse region details.
+
+=cut
+sub parse_region_details {
+    my ($region_details) = @_;
+    unless ($region_details =~ /(.+)\.rs(\d+)\.re(\d+)/) {
+        die "Issues with the seq region details";
+    }
+    return ($1, $2, $3);
+}
+
+
+=head2 sort_transcripts_by_slice
+
+NOT used
+
+=cut
+sub sort_transcripts_by_slice {
+    my ($transcripts) = @_;
+    my %sorted_transcript_hash;
+    #checks if there's already an arrayref associated with the current transcript's seq_region_name.
+    #If it's not defined (or evaluates to false), it assigns an empty arrayref [] to it.
+    #then pushes the current transcript onto the array corresponding to its seq_region_name.
+    push @{$sorted_transcript_hash{$_->seq_region_name} //= []}, $_ foreach @$transcripts;
+
+    return \%sorted_transcript_hash;
+}
+
+
+=head2 build_translation
+
+Process translation corrds to build translation and calculate exon phases.
+
+=cut
+sub build_translation {
+    my ($transcript, $translation_coords) = @_;
+
+    unless ($translation_coords =~ /(\d+):(\d+):(\d+):(\d+):(\d+):(\d+)/) {
+        throw("Issue parsing translation coords, coords string:\n$translation_coords");
+    }
+    my ($start_exon_start, $start_exon_end, $start_exon_offset, $end_exon_start, $end_exon_end, $end_exon_offset) = ($1, $2, $3, $4, $5, $6);
+    my $exons = $transcript->get_all_Exons();
+    my ($start_exon, $end_exon);
+    foreach my $exon (@$exons) {
+        if ($exon->start() == $start_exon_start && $exon->end() == $start_exon_end) {
+            $start_exon = $exon;
+        }
+        if ($exon->start() == $end_exon_start && $exon->end() == $end_exon_end) {
+            $end_exon = $exon;
+        }
+    unless ($start_exon && $end_exon) {
+        throw("Could not find matching start/end exon from the translation coords, translation coords:\n$translation_coords");
+    }
+
+    my $translation = set_translation($start_exon,  $end_exon);
+    $translation->start($start_exon_offset);
+    $translation->end($end_exon_offset);
+    $transcript->translation($translation);
+    calculate_exon_phases($transcript, 0);
+}