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gtf2gff3
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#!/usr/bin/perl
use strict;
use warnings;
use lib qw(/home/ruping/packages/CPAN//lib/perl5/site_perl/5.8.4/);
use Getopt::Long;
use Config::Std;
#-----------------------------------------------------------------------------
#----------------------------------- MAIN ------------------------------------
#-----------------------------------------------------------------------------
my $usage = "
Synopsis:
gtf2gff3 --cfg gtf2gff3_MY_CONFIG.cfg gtf_file > gff3_file
gtf2gff3 --help # for a more detailed help message.
Description:
This script will convert GTF formatted files to valid GFF3 formatted
files. It will map the column 3 (\"type\" column) to valid SO, but
because any non standard term may appear in that column in GTF files,
you may edit the config file to provide your own GTF feature to SO
mapping. The script will also build gene models from exons, CDSs and
other features given in the GTF file. It is currently tested on Ensemble
and Twinscan GTF, and it should work on any other files that follow the
same specification. It does not work on GTF from the UCSC table browser
because those files use the same ID for gene and transcript, so it is
impossible to group multiple transcripts to a gene. See the README that
came with the script for more info.
Options:
--cfg Provide the filename for a config file. See the configuration
file provided with this script for format details. Use this
configuration file to modify the behavior of the script. If no config
file is given it looks for ./gtf2gff3.cfg, ~/gtf2gff3.cfg or
/etc/gtf2gff3.cfg in that order.
--help Provide a more detailed help message.
";
my ($help, $cfg_file);
my $opt_success = GetOptions('help' => \$help,
'cfg=s' => \$cfg_file);
die $usage if ! $opt_success;
if ($help) {
print `perldoc $0`;
exit;
}
my $file = shift;
die $usage unless $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;
################################################################################
# LOAD CONFIGURATION OR USE DEFAULTS
################################################################################
read_config $cfg_file => my %config if -e $cfg_file;
our $INPUT_FEATURE_MAP = $config{INPUT_FEATURE_MAP};
$INPUT_FEATURE_MAP ||= {gene => 'gene',
mRNA => 'mRNA',
exon => 'exon',
five_prime_UTR => 'five_prime_utr',
start_codon => 'start_codon',
CDS => 'CDS',
stop_codon => 'stop_codon',
three_prime_UTR => 'three_prime_utr'};
our $GTF_ATTRB_MAP = $config{GTF_ATTRB_MAP};
$GTF_ATTRB_MAP ||= {gene_id => 'gene_id',
gene_name => 'gene_name',
trnsc_id => 'transcript_id',
trnsc_name => 'transcript_name'};
our $GFF3_ATTRB_MAP = $config{GFF3_ATTRB_MAP};
$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 $LIMIT_ATTRB = $config{MISC}{LIMIT_ATTRB} || 1;
our $ATTRB_DELIMITER = qr{$config{MISC}{ATTRB_DELIMITER}} || qr{\s*;\s*};
our $ATTRB_REGEX = qr{$config{MISC}{ATTRB_REGEX}} ||
qr{^\s*(\S+)\s+(\"[^\"]*\")\s*$};
our $START_IN_CDS = $config{MISC}{START_IN_CDS} || 1;
our $STOP_IN_CDS = $config{MISC}{STOP_IN_CDS} || 0;
our $DEFAULT_STRAND = $config{MISC}{DEFAULT_STRAND};
################################################################################
my ($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 die "FATAL: Can't open GTF file: $file for reading.\n$!\n";
# %genes will have the following structure:
# $genes->gene_id->trnsc_id->feature_type->feature
# |
# ->other->feature_type->feature
#
my (%genes, %features);
while (<$IN>) {
chomp;
s/^\s+//;
s/\s+$//;
#Handle full line comments, meta-comments and blank lines;
#Grab any comments
my ($comment) = $_ =~ s/(\#.*$)//;
;
my ($seqname, $source, $feature_type, $start, $end, $score,
$strand, $frame, $attrb_text) = split "\t", $_;
my $attributes = parse_attributes($attrb_text);
$feature_type = $INPUT_FEATURE_MAP->{$feature_type};
#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];
push @{$genes{$seqname}{$gene_id}{$trnsc_id}{$feature_type}},
$feature;
}
else {
push @{$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
return if ! defined $attrb_text || $attrb_text =~ /^\s+$/;
#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 $value !~ /\s/;
}
else {
print STDERR "ERROR: Missing or non-standard attributes: parse_attributes\n";
next ATT;
}
push @{$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
print STDERR "ERROR: Non-transcript gene feature " .
"not supported. Please contact the author for " .
"support: build_gene\n";
next TRN;
}
my $features = $trnscs->{$trnsc_id};
my $trnsc = build_trnsc($features);
push @trnscs, $trnsc;
}
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}) {
print STDERR "ERROR: Must have at least exons or CDSs to" .
"build a transcript: build_trnsc\n";
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 = {exon => $exons,
five_prime_UTR => $five_UTRs,
start_codon => $start,
CDS => $CDSs,
stop_codon => $stop,
three_prime_UTR => $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 {
die "FATAL: Need exons or CDSs to build transcripts: " .
"process_start.\n";
}
#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}) {
die "FATAL: Untested code in process_start. Contact the aurthor for support\n";
$five_UTRs = sort_features($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
# die "FATAL: Invalid feature set: process_start\n";
}
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 {
die "FATAL: Need exons or CDSs to build transcripts: " .
"process_stop\n";
}
#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}) {
$CDSs = sort_features($CDSs, $strand);
my $last_CDS = $CDSs->[-1];
$exons = sort_features($exons, $strand);
my $last_exon = $exons->[0];
if ($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 $stop_codon_end;
}
elsif (scalar @{$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}) {
die("FATAL: Untested code: process_stop.\n");
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
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, $three_UTRs);
}
else {
die "FATAL: Invalid feature set: process_exon_CDS_UTR\n";
}
return ($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
elsif (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
elsif (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);
for my $CDS (@{$CDSs}) {
my $exon = {start => $CDS->{start},
end => $CDS->{end},
type => 'exon',
score => '.',
strand => $strand,
phase => '.'};
#START_IN_CDS and STOP_IN_CDS were already considered when start and stop were
#constructed and CDSs were adjusted in include_terminal_codons
=head1
if ($i == 0 &&
$START_IN_CDS == 0) {
if ($strand == 1) {
$exon->start = $start->[0]{start};
}
else {
$exon->end = $start->[0]{end};
}
}
if ($i == (scalar @{$CDSs} - 1) &&
$STOP_IN_CDS == 0) {
if ($strand == 1) {
$exon->{end} = $stop->[0]{end};
}
else {
$exon->{start} = $stop->[0]{start}
}
}
=cut
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) {
$merged_exons[-1]{end} = $exon->{end};
}
else {
push @merged_exons, $exon;
}
}
return \@merged_exons;
}
#-----------------------------------------------------------------------------
sub validate_and_finish_trnsc {
my $features = shift;
my ($seq_id, $source, $strand, $gene_id, $gene_name,
$trnsc_id, $trnsc_name);
#Find default parameters from either exons or CDSs
TYPE:
for my $type ( qw|exon CDS| ) {
for my $feature (@{$features->{$type}}) {
$seq_id ||= $feature->{seq_id};
$source ||= $feature->{source};
$strand ||= $feature->{strand};
$gene_id ||=
$feature->{attributes}{$GTF_ATTRB_MAP->{gene_id}};
$gene_name ||=
$feature->{attributes}{$GTF_ATTRB_MAP->{gene_name}};
$trnsc_id ||=
$feature->{attributes}{$GTF_ATTRB_MAP->{trnsc_id}};
$trnsc_name ||=
$feature->{attributes}{$GTF_ATTRB_MAP->{trnsc_name}};
last TYPE if ! grep {! defined $_} ($seq_id, $source,
$strand, $gene_name,
$trnsc_id, $trnsc_name);
}
}
#Flag if we have any coding features (CDS, start_codon, stop_codon)
my $coding_flag;
#Min and max for transcript boundaries
my ($min, $max);
for my $feature_type (keys %{$features}) {
my $count;
#For keeping track of the phase for the next CDS.
my $next_phase = '.';
#Sort the features
$features->{$feature_type} =
sort_features($features->{$feature_type},
strand($strand));
for my $feature (@{$features->{$feature_type}}) {
#min and max to calculate transcript boundaries
$min = ! defined $min ?
$feature->{start} :
$min > $feature->{start} ?
$feature->{start} :
$min;
$max = ! defined $max ?
$feature->{end} :
$max < $feature->{end} ?
$feature->{end} :
$max;
#Set the flag if we see indications of coding features
if (grep {$feature_type eq $_} qw(CDS start_codon
stop_codon)) {
$coding_flag++ if $feature->{start};
}
#Calculate CDS phases.
if ($feature_type eq 'CDS') {
($feature, $next_phase) = CDS_phase($feature, $next_phase);
}
#Set parameters to defaults for all features that
#don't already have them set
if (! defined $feature->{seq_id}) {
$feature->{seq_id} = $seq_id;
}
elsif ($feature->{seq_id} ne $seq_id) {
print STDERR "ERROR: seq_id conflict: " .
"validate_and_finish_trnsc\n";
}
if (! defined $feature->{source}) {
$feature->{source} = $source;
}
elsif ($feature->{source} ne $source) {
print STDERR "ERROR: source conflict: " .
"validate_and_finish_trnsc\n";
}
if (! defined $feature->{type}) {
$feature->{type} = $feature_type;
}
elsif ($feature->{type} ne $feature_type) {
print STDERR "ERROR: type conflict: " .
"validate_and_finish_trnsc\n";
}
if (! defined $feature->{strand}) {
$feature->{strand} = $strand;
}
elsif ($feature->{strand} ne $strand) {
print STDERR "ERROR: strand conflict: " .
"validate_and_finish_trnsc\n";
}
if (! defined $feature->{score}) {
$feature->{score} = '.';
}
if (! defined $feature->{phase}) {
$feature->{phase} = '.';
}
#Set attributes
$feature->{attributes} =
{parent => $trnsc_id,
id => ["$feature_type:" . $trnsc_id->[0] .
":" . ++$count]};
}
}
my $trnsc_type = $coding_flag ? 'mRNA' : 'transcript';
my $attributes = {parent => $gene_id,
parent_name => $gene_name,
id => $trnsc_id,
name => $trnsc_name};
my $trnsc = {seq_id => $seq_id,
source => $source,
type => $trnsc_type,
start => $min,
end => $max,
score => '.',
strand => $strand,
phase => '.',
attributes => $attributes,
features => $features};
return $trnsc;
}
#-----------------------------------------------------------------------------
sub CDS_phase {
my ($feature, $next_phase) = @_;
#If phase isn't already valid assign it
if (! defined $feature->{phase} ||
$feature->{phase} !~ /^0|1|2$/) {
$feature->{phase} = $next_phase;
}
#If phase is valid, calculate the next phase
if ($feature->{phase} =~ /^0|1|2$/) {
my $length = ($feature->{end} -
$feature->{start}) + 1;
# my $hang_3 = $length % 3; # 3' overhang
# my $hang_5 = 3 - $hang_3; # 5' overhang
#
# #The next phase is equal to this phase
# #plus the modulus 3 of the length wrapped
# #at 2.
# $next_phase = $feature->{phase} + $hang_5;
# $next_phase -= 3 if $next_phase > 2;
# This was update 5/24/10 in response to an
# e-mail from Leighton Prichard regarding
# errors in the GFF3 spec. The code above
# calculates the phase correctly, but the
# formula suggested by Leighton is cleaner.
$next_phase = ($feature->{phase} - $length) % 3;
}
return ($feature, $next_phase);