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gtf2gff3
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#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
use Config::Std;
#-----------------------------------------------------------------------------
#----------------------------------- MAIN ------------------------------------
#-----------------------------------------------------------------------------
my $usage = "
Synopsis:
gtf2gff3 --cfg gtf2gff3_MY_CONFIG.cfg gtf_file > gff3_file
gtf2gff3 --help # for a more detailed help message.
Description:
This script will convert GTF formatted files to valid GFF3 formatted
files. It will map the column 3 (\"type\" column) to valid SO, but
because any non standard term may appear in that column in GTF files,
you may edit the config file to provide your own GTF feature to SO
mapping. The script will also build gene models from exons, CDSs and
other features given in the GTF file. It is currently tested on Ensemble
and Twinscan GTF, and it should work on any other files that follow the
same specification. It does not work on GTF from the UCSC table browser
because those files use the same ID for gene and transcript, so it is
impossible to group multiple transcripts to a gene. See the README that
came with the script for more info.
Options:
--cfg
Provide the filename for a config file. See the configuration
file provided with this script for format details. Use this
configuration file to modify the behavior of the script. If no
config file is given it looks for ./gtf2gff3.cfg, ~/gtf2gff3.cfg
or /etc/gtf2gff3.cfg in that order.
--print_cfg
Print a copy of the config variables as currently set (including
those set by --cfg) to STDOUT. This output can be used as the
starting point for creating a custom config file.
--help Provide a more detailed help message.
";
my ($help, $cfg_file, $print_cfg);
my $opt_success;
eval{$opt_success = GetOptions('help' => \$help,
'cfg=s' => \$cfg_file,
'print_cfg' => \$print_cfg)};
handle_message('FATAL', 'invalid_options', $@) unless $opt_success;
if ($help || !@ARGV) {
#print `perldoc $0`;
print $usage;
exit;
}
my $file = shift;
if (! $print_cfg) {
if (! defined $file) {
handle_message('FATAL', 'missing_gtf_file');
}
elsif (! -e $file) {
handle_message('FATAL', 'file_does_not_exist', $file);
}
elsif (! -r $file) {
handle_message('FATAL', 'file_not_readable', $file);
}
}
my $home = $ENV{HOME} || '.'; #Apache has no home, so avoid the error.
my @cfg_files = ($cfg_file,
'./gtf2gff3.cfg',
"$home/gtf2gff3.cfg",
'/etc/gtf2gff3.cfg',
);
@cfg_files = grep {-e $_ if $_} @cfg_files;
$cfg_file = shift @cfg_files;
$cfg_file ||= '';
################################################################################
# LOAD CONFIGURATION OR USE DEFAULTS
################################################################################
my %config;
if ($cfg_file) {
handle_message('FATAL', 'unreadable_file', $cfg_file) unless -r $cfg_file;
eval {
require Config::Std;
};
if ($@ =~ /Can\'t locate/) {
handle_message('WARN', 'missing_dependency', 'Config::Std not installed. Using internal defaults.');
}
else {
read_config($cfg_file => %config);
}
}
# Use INPUT_FEATURE_MAP to map GTF feature types (column 3 in GTF) to valid SO types.
# Don't edit the SO terms below. Mapping must be many to one. That means that
# exon_this and exon_that could both map to the SO term exon, but exon_this
# could not map to multiple SO terms.
# GTF Term (maps to) #SO Term
$config{INPUT_FEATURE_MAP} ||= {"3'-UTR" => 'three_prime_UTR',
'3UTR' => 'three_prime_UTR',
"5'-UTR" => 'five_prime_UTR',
'5UTR' => 'five_prime_UTR',
ARS => 'ARS',
binding_site => 'binding_site',
BLASTN_HIT => 'nucleotide_match',
CDS => 'CDS',
CDS_motif => 'nucleotide_motif',
CDS_parts => 'mRNA_region',
centromere => 'centromere',
chromosome => 'chromosome',
conflict => 'conflict',
Contig => 'contig',
exon => 'exon',
five_prime_utr => 'five_prime_UTR',
five_prime_UTR => 'five_prime_UTR',
gene => 'gene',
insertion => 'insertion',
intron => 'intron',
LTR => 'long_terminal_repeat',
misc_feature => 'sequence_feature',
misc_RNA => 'transcript',
mRNA => 'mRNA',
nc_primary_transcript => 'nc_primary_transcript',
ncRNA => 'ncRNA',
nucleotide_match => 'nucleotide_match',
polyA_signal => 'polyA_signal_sequence',
polyA_site => 'polyA_site',
promoter => 'promoter',
pseudogene => 'pseudogene',
real_mRNA => 'mRNA',
region => 'region',
repeat_family => 'repeat_family',
repeat_region => 'repeat_region',
repeat_unit => 'repeat_region',
rep_origin => 'origin_of_replication',
rRNA => 'rRNA',
Selenocysteine => 'selenocysteine',
snoRNA => 'snoRNA',
snRNA => 'snRNA',
source => 'sequence_feature',
start_codon => 'start_codon',
start_codon => 'start_codon',
stop_codon => 'stop_codon',
stop_codon => 'stop_codon',
telomere => 'telomere',
three_prime_utr => 'three_prime_UTR',
three_prime_UTR => 'three_prime_UTR',
transcript_region => 'transcript_region',
transcript => 'transcript',
transposable_element_gene => 'transposable_element',
transposable_element => 'transposable_element',
tRNA => 'tRNA',
tss => 'TSS',
TSS => 'TSS',
tts => 'transcription_end_site',
TTS => 'transcription_end_site',
UTR => 'UTR',
};
our $INPUT_FEATURE_MAP = $config{INPUT_FEATURE_MAP};
# Maps tags used internally to tags found in your GTF file
# Don't edit the code tags.
# Note that the gene_id and transcript_id tags tell the script
# who the parents of a feature are.
# Code Tag (comes from) #GTF Tag
$config{GTF_ATTRB_MAP} ||= {gene_id => 'gene_id',
gene_name => 'gene_name',
trnsc_id => 'transcript_id',
trnsc_name => 'transcript_name'};
our $GTF_ATTRB_MAP = $config{GTF_ATTRB_MAP};
# Maps tags used internally to output GFF3 attribute tags.
# Also, when LIMIT_ATTRB is set to 1 only these tags will be
# Output to the GFF3 attributes column.
# Code Tag #GFF3 Tag
$config{GFF3_ATTRB_MAP} ||= {gene_id => 'gene_id',
gene_name => 'gene_name',
trnsc_id => 'transcript_id',
trnsc_name => 'transcript_name',
id => 'ID',
parent => 'Parent',
name => 'Name'};
our $GFF3_ATTRB_MAP = $config{GFF3_ATTRB_MAP};
# Limit the attribute tags printed to only those in the GFF3_ATTRB_MAP
$config{MISC}{LIMIT_ATTRB} ||= 0;
our $LIMIT_ATTRB = $config{MISC}{LIMIT_ATTRB};
# A perl regexp that splits the attributes column into seperate attributes.
$config{MISC}{ATTRB_DELIMITER} ||= qr{\s*;\s*};
our $ATTRB_DELIMITER = $config{MISC}{ATTRB_DELIMITER};
# A perl regexp that captures the tag value pairs.
$config{MISC}{ATTRB_REGEX} ||= qr{^\s*(\S+)\s+(\"?[^\"]*\"?)\s*$};
our $ATTRB_REGEX = $config{MISC}{ATTRB_REGEX};
# If CDSs are annotated in the GTF file, are the start codons already included (1=yes 0=no)
$config{MISC}{START_IN_CDS} = defined $config{MISC}{START_IN_CDS} ? $config{MISC}{START_IN_CDS} : 1;
our $START_IN_CDS = $config{MISC}{START_IN_CDS};
# If CDSs are annotated in the GTF file, are the stop codons already included (1=yes 0=no)
$config{MISC}{STOP_IN_CDS} = defined $config{MISC}{STOP_IN_CDS} ? $config{MISC}{STOP_IN_CDS} : 0;
our $STOP_IN_CDS = $config{MISC}{STOP_IN_CDS};
# Use the following value (+ or -) for a features strand as the default if an invalid value is passed.
$config{MISC}{DEFAULT_STRAND} = defined $config{MISC}{DEFAULT_STRAND} ? $config{MISC}{DEFAULT_STRAND} : '+';
our $DEFAULT_STRAND = $config{MISC}{DEFAULT_STRAND};
################################################################################
print_config(\%config) if $print_cfg;
my @META_DATA;
my ($genes, $features) = parse_gtf($file);
$genes = build_genes($genes);
print_gff3($genes, $features);
#-----------------------------------------------------------------------------
#-------------------------------- SUBROUTINES --------------------------------
#-----------------------------------------------------------------------------
sub parse_gtf {
my $file = shift;
open (my $IN, '<', $file) or
handle_message('FATAL', 'cant_open_file_for_reading', $file);
# %genes will have the following structure:
# $genes->gene_id->trnsc_id->feature_type->feature
# |
# ->other->feature_type->feature
#
my (%genes, %features);
LINE:
while (my $line = <$IN>) {
chomp $line;
$line =~ s/^\s+//;
$line =~ s/\s+$//;
next LINE unless $line;
#Handle full line comments, meta-comments and blank lines;
if ($line =~ /^\#/) {
if ($line =~ /^\#\#gff-version\s+3/) {
handle_message('FATAL', 'file_claims_to_be_gff3', $line);
}
$line =~ s/^\#+/\#/;
push @META_DATA, $line;
next LINE;
}
#Grab any comments
my ($comment) = $line =~ s/(\#.*)$//;
my @columns = split /\t/, $line;
handle_message('FATAL', 'too_many_columns_for_gtf_data', $line)
unless scalar @columns == 9;
my ($seqname, $source, $feature_type, $start, $end, $score,
$strand, $frame, $attrb_text) = @columns;
handle_message('FATAL', 'invalid_start', $line)
unless $start =~ /^\d+$/;
handle_message('FATAL', 'invalid_end', $line)
unless $end =~ /^\d+$/;
handle_message('WARN', 'missing_attribute_text', $line)
unless $attrb_text;
my $attributes = parse_attributes($attrb_text);
if (! scalar keys %{$attributes}) {
handle_message('WARN', 'failed_to_parse_attributes', $line);
}
if (exists $INPUT_FEATURE_MAP->{$feature_type}) {
$feature_type = $INPUT_FEATURE_MAP->{$feature_type};
}
else {
handle_message('WARN', 'cant_map_feature_type', $feature_type);
$feature_type = 'sequence_feature';
}
#Note here that we're mapping between GTF/GFF and GFF3
#nomeclature for the hash keys
my $feature = {seq_id => $seqname,
source => $source,
type => $feature_type,
start => $start,
end => $end,
score => $score,
strand => $strand,
phase => $frame,
attributes => $attributes,
comment => $comment};
#Feature has a gene_id
if (exists $attributes->{$GTF_ATTRB_MAP->{gene_id}}) {
my $gene_id = $attributes->{$GTF_ATTRB_MAP->{gene_id}}[0];
#Feature has a gene ID and transcript ID
if (exists $attributes->{$GTF_ATTRB_MAP->{trnsc_id}}) {
my $trnsc_id = $attributes->{$GTF_ATTRB_MAP->{trnsc_id}}[0];
# fix broken UCSC GTF!
#if ($gene_id eq $trnsc_id) {
# ($gene_id = $trnsc_id) =~ s/\.\d+$//;
# $attributes->{gene_id}[0] = $gene_id;
#}
push @{$genes{$seqname}{$gene_id}{$trnsc_id}{$feature_type}},
$feature;
}
# Feature is a gene
elsif ($feature->{type} eq 'gene') {
# Do nothing
}
else {
push @{$genes{$seqname}{$gene_id}{other}{$feature}},
$feature;
}
}
else {
push @{$features{$feature_type}}, $feature;
}
}
return (\%genes, \%features);
}
#-----------------------------------------------------------------------------
sub parse_attributes {
my $attrb_text = shift;
#Skip it if it's undefined or empty
if (! defined $attrb_text || $attrb_text =~ /^\s+$/) {
handle_message('WARN', 'empty_attribute_text');
return {};
}
#Split the attributes
my @attrb_array = split $ATTRB_DELIMITER, $attrb_text;
#Grab key, value pairs
my %attributes;
ATT:
for my $attrb (@attrb_array) {
my ($key, $value);
if ($attrb =~ $ATTRB_REGEX) {
($key, $value) = ($1, $2);
$value =~ s/\"//g if $value !~ /\s/;
}
elsif (! $attrb) {
handle_message('WARN', 'empty_attribute',
'Check $ATTRB_DELIMITER in the config file ' .
'to match: ' . $attrb_text);
next ATT;
}
else {
handle_message('WARN', 'attribute_regex_doesnt_match',
'Check $ATTRB_REGEX in the config file ' .
'to match: ' . $attrb);
next ATT;
}
push @{$attributes{$key}}, $value;
}
return \%attributes;
}
#-----------------------------------------------------------------------------
sub build_genes {
my $genes = shift;
my @genes;
for my $seq_id (keys %{$genes}) {
for my $gene_id (keys %{$genes->{$seq_id}}) {
my $gene = build_gene($genes->{$seq_id}{$gene_id});
push @genes, $gene;
}
}
return \@genes;
}
#-----------------------------------------------------------------------------
sub build_gene {
my $trnscs = shift;
my @trnscs;
TRN:
for my $trnsc_id (keys %{$trnscs}) {
if ($trnsc_id eq 'other') {
#Handle non-transcript gene features
handle_message('WARN', 'non-transcript_gene_feature',
'Non-transcript gene features' .
'are not currently supported.' .
'Please contact the author for' .
'support.');
next TRN;
}
my $features = $trnscs->{$trnsc_id};
my $trnsc = build_trnsc($features);
if ($trnsc) {
push @trnscs, $trnsc;
}
else {
handle_message('WARN', 'transcript_not_built', $trnsc_id);
}
}
my $gene = validate_and_build_gene(\@trnscs);
return $gene;
}
#-----------------------------------------------------------------------------
sub build_trnsc {
my $features = shift;
my $exons = $features->{exon} || [];
my $CDSs = $features->{CDS} || [];
my $start = $features->{start_codon} || [];
my $stop = $features->{stop_codon} || [];
my $five_UTRs = $features->{five_prime_UTR} || [];
my $three_UTRs = $features->{three_prime_UTR} || [];
#We require at least CDSs or exons
unless (scalar @{$CDSs} || scalar @{$exons}) {
handle_message('WARN', 'must_have_exons_or_CDS_to_build_transcript',
join ", ", keys %{$features});
return;
}
#Make start codons if they don't exist
$start = process_start($exons, $CDSs, $start, $five_UTRs)
if ! scalar @{$start};
#Make stop codons if they don't exist
$stop = process_stop($exons, $CDSs, $stop, $three_UTRs)
if ! scalar @{$stop};
#Make UTRs, exons and/or CDSs if they don't exist
($five_UTRs,
$exons,
$CDSs,
$three_UTRs) = process_exon_CDS_UTRs($exons, $CDSs,
$start, $stop,
$five_UTRs,
$three_UTRs);
@{$features}{qw(exon five_prime_UTR start_codon CDS stop_codon
three_prime_UTR)} =
($exons, $five_UTRs, $start, $CDSs,
$stop, $three_UTRs);
#Build and validate the transcripts
my $trnsc = validate_and_finish_trnsc($features);
return $trnsc;
}
#-----------------------------------------------------------------------------
sub process_start {
my ($exons, $CDSs, $start, $five_UTRs) = @_;
my ($start_codon_start, $start_codon_end);
my $strand;
#Get the strand for exons or CDSs
if (scalar @{$exons}) {
$strand = strand($exons->[0]->{strand});
}
elsif (scalar @{$CDSs}) {
$strand = strand($CDSs->[0]->{strand});
}
else {
handle_message('WARN', 'need_exons_or_cdss_to_build_transcripts');
}
#Already have start
if (scalar @{$start}) {
return $start;
}
################################################################################
# Don't infer start codons from CDS unless backed by UTR or exon infered UTR
################################################################################
#Build start from CDS
elsif (scalar @{$CDSs} && scalar @{$exons}) {
$CDSs = sort_features($CDSs, $strand);
my $first_CDS = $CDSs->[0];
$exons = sort_features($exons, $strand);
my $first_exon = $exons->[0];
if ($strand == 1) {
if ($first_exon->{start} < $first_CDS->{start}) {
$start_codon_start = $first_CDS->{start};
#Move start codon out of CDS if config says to
if ($START_IN_CDS == 0) {
$start_codon_start -= 3;
}
}
}
elsif ($strand == -1) {
if ($first_exon->{end} > $first_CDS->{end}) {
$start_codon_start = $first_CDS->{end} - 2;
#Move start codon out of CDS if config says to
if ($START_IN_CDS == 0) {
$start_codon_start += 3;
}
}
}
$start_codon_end = $start_codon_start + 2
if defined $start_codon_start;
}
#Here we assume that if you have 5' UTR and CDS that the start codon
#must be at the begining of the first CDS. To be more rigorous we should
#check the coordinates and be sure that the 5' UTR and CDS are contiguous.
elsif (scalar @{$CDSs} && scalar @{$five_UTRs}) {
$CDSs = sort_features($CDSs, $strand);
my $first_CDS = $CDSs->[0];
if ($strand == 1) {
$start_codon_start = $first_CDS->{start};
#Move start codon out of CDS if config says to
if ($START_IN_CDS == 0) {
$start_codon_start -= 3;
}
}
elsif ($strand == -1) {
$start_codon_start = $first_CDS->{end} - 2;
#Move start codon out of CDS if config says to
if ($START_IN_CDS == 0) {
$start_codon_start += 3;
}
}
$start_codon_end = $start_codon_start + 2;
}
#Build start from UTRs - I haven't seen an example of this yet. Maybe I should
#only create a start codon if it falls within an exon or CDS.
elsif (scalar @{$five_UTRs}) {
handle_message('FATAL', 'untested_code', 'The subroutine ' .
'process_start has run into data it doesnt know ' .
'how to handle. Please contact the aurthor for ' .
'support if you see this message');
$five_UTRs = sort_features($five_UTRs, $strand);
my $last_five_UTR = $five_UTRs->[-1];
$start_codon_start = $strand == 1 ? $last_five_UTR->{start} + 1 :
$last_five_UTR->{end} - 3;
$start_codon_end = $start_codon_start + 2;
}
#No CDSs or UTRs - let's pretend it's non-coding
elsif (scalar @{$exons}) {
return [];
}
else {
return [];
# We don't really need to die here some annotations have
# stop_codon, but not start_codon
}
return [] if (! defined $start_codon_start ||
! defined $start_codon_end);
$start = [{start => $start_codon_start,
end => $start_codon_end,
type => 'start_codon',
score => '.',
phase => '0'}];
return $start;
}
#-----------------------------------------------------------------------------
sub process_stop {
my ($exons, $CDSs, $stop, $three_UTRs) = @_;
my ($stop_codon_start, $stop_codon_end);
#Get the strand
my $strand;
if (scalar @{$exons}) {
$strand = strand($exons->[0]->{strand});
}
elsif (scalar @{$CDSs}) {
$strand = strand($CDSs->[0]->{strand});
}
else {
handle_message('WARN', 'need_exons_or_cdss_to_build_transcripts');
}
#If we already have a stop then return it.
if (scalar @{$stop}) {
return $stop;
}
################################################################################
# Don't infer stop codons from CDS unless backed by UTR or exon infered UTR
################################################################################
#Build stop from CDSs
elsif (scalar @{$CDSs} && scalar @{$exons}) {
$CDSs = sort_features($CDSs, $strand);
my $last_CDS = $CDSs->[-1];
$exons = sort_features($exons, $strand);
my $last_exon = $exons->[-1];
if ($strand == 1) {
if ($last_exon->{end} > $last_CDS->{end}) {
$stop_codon_start = $last_CDS->{end} - 2;
#Move stop codon out of CDS is config says to
if ($STOP_IN_CDS == 0) {
$stop_codon_start += 3;
}
}
}
elsif ($strand == -1) {
if ($last_exon->{start} < $last_CDS->{start}) {
$stop_codon_start = $last_CDS->{start};
#Move stop codon out of CDS is config says to
if ($STOP_IN_CDS == 0) {
$stop_codon_start -= 3;
}
}
}
$stop_codon_end = $stop_codon_start + 2
if defined $stop_codon_start;
}
elsif (scalar @{$CDSs} && scalar @{$three_UTRs}) {
$CDSs = sort_features($CDSs, $strand);
my $last_CDS = $CDSs->[-1];
if ($strand == 1) {
$stop_codon_start = $last_CDS->{end} - 2;
#Move stop codon out of CDS is config says to
if ($STOP_IN_CDS == 0) {
$stop_codon_start += 3;
}
}
elsif ($strand == -1) {
$stop_codon_start = $last_CDS->{start};
#Move stop codon out of CDS is config says to
if ($STOP_IN_CDS == 0) {
$stop_codon_start -= 3;
}
}
$stop_codon_end = $stop_codon_start + 2;
}
#Build stop from UTRs
elsif (scalar @{$three_UTRs}) {
handle_message('FATAL', 'untested_code', 'The subroutine ' .
'process_stop has run into data it doesn\'t know ' .
'how to handle. Please contact the aurthor for ' .
'support if you see this message');
my $strand = strand($three_UTRs->[0]);
$three_UTRs = sort_features($three_UTRs, $strand);
my $first_three_UTR = $three_UTRs->[0];
$stop_codon_start = $strand == 1 ? $first_three_UTR->{start} - 3 :
$first_three_UTR->{end} + 1;
$stop_codon_end = $stop_codon_start + 2;
}
elsif (scalar @{$exons}) {
#Treating this as a non-coding transcript
return [];
}
else {
# We don't really need to die here. Some features may have
# start_codon, but not stop_codon
handle_message('WARN', 'cant_infer_stop');
return [];
#die "FATAL : Invalid feature set : process_stop\n";
}
return [] if (! defined $stop_codon_start ||
! defined $stop_codon_end);
$stop = [{start => $stop_codon_start,
end => $stop_codon_end,
type => 'stop_codon',
score => '.',
phase => '0'}];
return $stop;
}
#-----------------------------------------------------------------------------
sub process_exon_CDS_UTRs {
my ($exons, $CDSs, $start, $stop,
$five_UTRs, $three_UTRs) = @_;
#Check what features we already have so we don't rebuild them
my $have_five_UTRs++ if scalar @{$five_UTRs};
my $have_exons++ if scalar @{$exons};
my $have_start++ if scalar @{$start};
my $have_CDSs++ if scalar @{$CDSs};
my $have_stop++ if scalar @{$stop};
my $have_three_UTRs++ if scalar @{$three_UTRs};
#If CDSs already exist make sure that they include start and stop codons
if (scalar @{$CDSs}) {
include_terminal_codons($CDSs, $start, $stop);
}
#If we already have everything, then return
if ($have_exons && $have_CDSs && ($have_five_UTRs || $have_three_UTRs)) {
return ($five_UTRs, $exons, $CDSs, $three_UTRs);
}
#Build CDSs && UTRs
elsif ($have_exons && ($have_start || $have_stop || $have_CDSs ||
$have_three_UTRs || $have_five_UTRs)) {
# Make sure that evaluate exons can handle only a start OR a stop!!!
for my $exon (@{$exons}) {
my ($five_UTR, $CDS, $three_UTR) =
evaluate_exon($exon, $start->[0], $stop->[0]);
push @{$five_UTRs}, $five_UTR
if scalar keys %{$five_UTR} && ! $have_five_UTRs;
push @{$CDSs}, $CDS if scalar keys %{$CDS} && ! $have_CDSs;
push @{$three_UTRs}, $three_UTR
if scalar keys %{$three_UTR} && ! $have_three_UTRs;
}
}
#Build exons
elsif (!$have_exons && $have_CDSs){
$exons = build_exons($five_UTRs, $start, $CDSs, $stop, $three_UTRs);
}
#Treat as non-coding even if we have a start or stop but not both
elsif ($have_exons && ! $have_CDSs && ! $have_five_UTRs &&
! $have_three_UTRs && ! $have_start && ! $have_stop) {
#Treating this as a non_coding transcript
return ($five_UTRs, $exons, $CDSs, $three_UTRs);
}
else {
handle_message('FATAL', 'invalid_feature_set',
'The subroutine process_exon_CDS_UTRs was given ' .
'a set of feature that it can\'t work with.');
}
return ($five_UTRs, $exons, $CDSs, $three_UTRs);
}
#-----------------------------------------------------------------------------
sub include_terminal_codons {
my ($CDSs, $start, $stop) = @_;
my $strand = strand($CDSs->[0]{strand});
$CDSs = sort_features($CDSs, $strand);
my $first_CDS = $CDSs->[0];
my $last_CDS = $CDSs->[-1];
if ($strand == 1) {
if (scalar @{$start}) {
$first_CDS->{start} = $start->[0]{start}
if $start->[0]{end} + 1 == $first_CDS->{start};
}
#START_IN_CDS was considered when start was built, so it could introduce errors
#to consider it again here
# elsif (defined $START_IN_CDS) {
# $first_CDS->{start} -= 3 if ! $START_IN_CDS;
# }
if (scalar @{$stop}) {
$last_CDS->{end} = $stop->[0]{end}
if $stop->[0]{start} - 1 == $last_CDS->{end};
}
#STOP_IN_CDS was considered when stop was built, so it could introduce errors
#to consider it again here
# elsif (defined $STOP_IN_CDS) {
# $last_CDS->{end} += 3 if ! $STOP_IN_CDS;
# }
}
elsif ($strand == -1) {
if (scalar @{$start}) {
$first_CDS->{end} = $start->[0]{end}
if $start->[0]{start} - 1 == $first_CDS->{end};
}
#START_IN_CDS was considered when start was built, so it could introduce errors
#to consider it again here
# elsif (defined $START_IN_CDS) {
# $first_CDS->{end} += 3 if ! $START_IN_CDS;
# }
if (scalar @{$stop}) {
$last_CDS->{start} = $stop->[0]{start}
if $stop->[0]{end} + 1 == $last_CDS->{start};
}
#STOP_IN_CDS was considered when stop was built, so it could introduce errors
#to consider it again here
# elsif (defined $STOP_IN_CDS) {
# $last_CDS->{start} -= 3 if ! $STOP_IN_CDS;
# }
}
}
#-----------------------------------------------------------------------------
sub evaluate_exon {
my ($exon, $start, $stop) = @_;
my $strand = strand($exon);
my %five_UTR;
my %CDS;
my %three_UTR;
#######################################
# Allow success if missing either start or stop
#######################################
if ($strand == 1) {
#Exon is fully 5' UTR
if (defined $start->{start} &&
$exon->{end} <= $start->{start}) {
$five_UTR{start} = $exon->{start};
$five_UTR{end} = $exon->{end};
}
#Exon stradles start codon
elsif (defined $start->{start} &&
$exon->{start} < $start->{start} &&
$exon->{end} > $start->{start} ) {
$five_UTR{start} = $exon->{start};
$five_UTR{end} = $start->{start} - 1;
if (defined $stop->{start}) {
$CDS{start} = $start->{start};
$CDS{end} = $exon->{end};
$CDS{phase} = 0;
}
}
#Exon is fully CDS
elsif (defined $start->{start} &&
defined $stop->{end} &&
$exon->{start} >= $start->{start} &&
$exon->{end} <= $stop->{end} ) {
$CDS{start} = $exon->{start};
$CDS{end} = $exon->{end};
#Set phase if this is first CDS
if ($exon->{start} == $start->{end} + 1 ||
$exon->{start} == $start->{start} ) {
$CDS{phase} = 0;
}
}
#Exon stradles stop codon
if (defined $stop->{end} &&
$exon->{start} < $stop->{end} &&
$exon->{end} > $stop->{end} ) {
$three_UTR{start} = $stop->{end} + 1;
$three_UTR{end} = $exon->{end};
if (defined $start->{start}) {
$CDS{start} = $exon->{start};
$CDS{end} = $stop->{end};
}
}
#Exon is fully 3' UTR
elsif (defined $stop->{end} &&
$exon->{start} >= $stop->{end}) {
$three_UTR{start} = $exon->{start};
$three_UTR{end} = $exon->{end};
}
else {
# die "Fatal error in evaluate_exon\n";
}
}
else {
#Exon is fully 5' UTR
if (defined $start->{end} &&
$exon->{start} >= $start->{end}) {
$five_UTR{start} = $exon->{start};
$five_UTR{end} = $exon->{end};
}
#Exon stradles start codon
elsif (defined $start->{end} &&
$exon->{start} < $start->{end} &&
$exon->{end} > $start->{end} ) {
$five_UTR{start} = $start->{end} + 1;
$five_UTR{end} = $exon->{end};
if (defined $stop->{start}) {
$CDS{start} = $exon->{start};
$CDS{end} = $start->{end};
}
$CDS{phase} = 0;
}
#Exon is fully CDS
elsif (defined $start->{end} &&
defined $stop->{start} &&
$exon->{end} <= $start->{end} &&
$exon->{start} >= $stop->{start} ) {
$CDS{start} = $exon->{start};
$CDS{end} = $exon->{end};
#Set phase 0 if this is first CDS
if ($exon->{end} == $start->{start} - 1 ||
$exon->{end} == $start->{end} ) {
$CDS{phase} = 0;
}
}
#Exon stradles stop codon
if (defined $stop->{start} &&
$exon->{end} > $stop->{start} &&
$exon->{start} < $stop->{start} ) {
$three_UTR{start} = $exon->{start};
$three_UTR{end} = $stop->{start} - 1;
if (defined $start->{end}) {
$CDS{start} = $stop->{start};
$CDS{end} = $exon->{end};
}
}
#Exon is fully 3' UTR
elsif (defined $stop->{start} &&
$exon->{end} <= $stop->{start}) {
$three_UTR{start} = $exon->{start};
$three_UTR{end} = $exon->{end};
}
else {
# die "Fatal error in evaluate_exon\n";
}
}
return (\%five_UTR, \%CDS, \%three_UTR);
}
#-----------------------------------------------------------------------------
sub build_exons {
my ($five_UTRs, $start, $CDSs, $stop, $three_UTRs) = @_;
my $strand = $CDSs->[0]{strand};
my @exons;
#Make an exon for every 5' UTR
for my $five_UTR (@{$five_UTRs}) {
push @exons, {start => $five_UTR->{start},
end => $five_UTR->{end},
type => 'exon',
score => '.',
strand => $strand,
phase => '.'};
}
#Make and exon for every CDS
$CDSs = sort_features($CDSs, $strand);
for my $CDS (@{$CDSs}) {
my $exon = {start => $CDS->{start},
end => $CDS->{end},
type => 'exon',
score => '.',
strand => $strand,
phase => '.'};
push @exons, $exon;
}
#Make an exon for every 3' UTR
for my $three_UTR (@{$three_UTRs}) {
push @exons, {start => $three_UTR->{start},
end => $three_UTR->{end},
type => 'exon',
score => '.',
strand => $strand,
phase => '.'};
}
# Merge any contiguous exons (i.e. from UTR & CDS neighbors)
my $exons = sort_features(\@exons, 1);
my @merged_exons = shift @{$exons};
while (my $exon = shift @{$exons}) {
if ($exon->{start} <= $merged_exons[-1]{end} + 1) {