diff --git a/modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm b/modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm
index b9b6214f35fbc897fbe75f940aa62545d6aea5c5..43114be8b3daa0fbc2dc1292603894c423f49097 100644
--- a/modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm
@@ -1,4 +1,3 @@
-
=pod
=head1 LICENSE
@@ -24,7 +23,6 @@ Monika Komorowska, 2012 - monika@ebi.ac.uk
use strict;
use Bio::EnsEMBL::Utils::IO::GFFParser;
-use Bio::EnsEMBL::Utils::Scalar qw/wrap_array/;
use FileHandle;
my $file_name = "features.gff";
@@ -47,21 +45,34 @@ while (defined($feature) ) {
#do something with the feature, e.g. print hash keys and values
foreach my $key (keys %feature) {
- if ($key ne 'attribute') {
- print $key . " " . $feature{$key} ."\n";
- } else {
- print $key . "\n";
- my %attribs = %{$feature{$key}};
- foreach my $attrib_key (keys %attribs) {
- my $values = $attribs{$attrib_key};
- printf("\t%s %s\n", $attrib_key, join(q{, }, @{wrap_array($values)}));
- }
- }
+ if ($key ne 'attribute') {
+ print $key . " " . $feature{$key} ."\n";
+ } else {
+ print $key . "\n";
+ my %attribs = %{$feature{$key}};
+ foreach my $attrib_key (keys %attribs) {
+ printf("\t%s %s\n", $attrib_key, join(q{, }, @{wrap_array($values)}));
+
+ }
+ }
}
print "\n\n";
$feature = $parser->parse_next_feature();
}
+my $sequence = $parser->parse_next_sequence();
+
+while (defined($sequence)) {
+ my %sequence = %{$sequence};
+
+ foreach my $key (keys %sequence) {
+ print $key . " " . $sequence{$key} ."\n";
+ }
+ print "\n\n";
+
+ $sequence = $parser->parse_next_sequence();
+}
+
$parser->close();
$fh->close();
@@ -70,7 +81,7 @@ $fh->close();
=head1 DESCRIPTION
-GFF3 format as defined in http://www.sequenceontology.org/gff3.shtml.
+GFF3 format as defined in http://www.sequenceontology.org/gff3.shtml
Use parse_header method to parse a GFF3 file header, and parse_next_feature to parse the next feature line in the file.
@@ -85,8 +96,10 @@ use warnings;
use Bio::EnsEMBL::Utils::Exception;
use IO::File;
use URI::Escape;
+use Bio::EnsEMBL::Utils::Scalar qw/wrap_array/;
+
-my %strand_conversion = ( '+' => '1', '?' => '0', '-' => '-1' );
+my %strand_conversion = ( '+' => '1', '?' => '0', '-' => '-1');
=head2 new
@@ -98,13 +111,15 @@ my %strand_conversion = ( '+' => '1', '?' => '0', '-' => '-1' );
=cut
sub new {
- my $class = shift;
- my $self = { filehandle => shift, };
- bless $self, $class;
- if ( !defined( $self->{'filehandle'} ) ) {
- throw("GFFParser requires a valid filehandle to a GFF3 formatted file");
- }
- return $self;
+ my $class = shift;
+ my $self = {
+ filehandle => shift,
+ };
+ bless $self, $class;
+ if (!defined($self->{'filehandle'})) {
+ throw("GFFParser requires a valid filehandle to a GFF3 formatted file");
+ }
+ return $self;
}
@@ -118,31 +133,31 @@ sub new {
sub parse_header {
- my $self = shift;
+ my $self = shift;
- my $next_line;
- my @header_lines;
-
- while ( ( $next_line = $self->_read_line() ) && ( $next_line =~ /^[\#|\s]/ ) )
- {
-
- #header lines start with ##
- if ( $next_line =~ /^[\#]{2}/ ) {
- push @header_lines, $next_line;
- if ( $next_line =~ /gff-version\s+(\d+)/ ) {
- if ( $1 != 3 ) {
- warning(
-"File has been formatted in GFF version $1. GFFParser may return unexpected results as it is designed to parse GFF3 formatted files."
- );
- }
- }
+ my $next_line;
+ my @header_lines;
+
+ while (($next_line = $self->_read_line()) && ($next_line =~ /^[\#|\s]/) ) {
+
+ #stop parsing features if ##FASTA directive encountered
+ last if ($next_line =~ /\#\#FASTA/ );
+
+ #header lines start with ## (except for the ##FASTA directive indicating sequence section)
+ if ($next_line =~ /^[\#]{2}/ ) {
+ push @header_lines, $next_line;
+ if ($next_line =~ /gff-version\s+(\d+)/) {
+ if ($1 != 3) {
+ warning("File has been formatted in GFF version $1. GFFParser may return unexpected results as it is designed to parse GFF3 formatted files.");
+ }
+ }
+ }
}
- }
- if ( defined($next_line) && ( $next_line !~ /^[\#|\s]/ ) ) {
- $self->{'first_feature_line'} = $next_line;
- }
- return \@header_lines;
+ if (defined($next_line)) {
+ $self->{'first_non_header_line'} = $next_line;
+ }
+ return \@header_lines;
}
@@ -162,93 +177,153 @@ sub parse_header {
attribute => hashref,
}
- If the attribute value held more than one value then we hold an arrayref
- not a scalar
Returntype : Hashref of a GFF3 feature line
=cut
sub parse_next_feature {
- my $self = shift;
+ my $self = shift;
- # my $next_line;
- my $feature_line;
-
- while ( my ($next_line) = $self->_read_line() ) {
- next
- if ( $next_line =~ /^\#/
- || $next_line =~ /^\s*$/
- || $next_line =~ /^\/\// );
- $feature_line = $next_line;
- last;
- }
-
- return undef unless $feature_line;
+ my $next_line;
+ my $feature_line;
+
+ while (($next_line = $self->_read_line() ) && defined($next_line) ) {
- my %feature;
- my %attribute;
+ #stop parsing features if ##FASTA directive
+ last if ($next_line =~ /\#\#FASTA/);
- #strip off trailing comments
- $feature_line =~ s/\#.*//;
- my @chunks = split( /\t/, $feature_line );
+ next if ($next_line =~ /^\#/ || $next_line =~ /^\s*$/ ||
+ $next_line =~ /^\/\//);
- %feature = (
- 'seqid' => uri_unescape( $chunks[0] ),
- 'source' => uri_unescape( $chunks[1] ),
- 'type' => uri_unescape( $chunks[2] ),
- 'start' => $chunks[3],
- 'end' => $chunks[4],
- 'score' => $chunks[5],
- 'strand' => $strand_conversion{ $chunks[6] },
- 'phase' => $chunks[7]
- );
+ $feature_line = $next_line;
+ last;
+ }
- if ( $chunks[8] ) {
+ return undef unless $feature_line;
+
+ my %feature;
+ my %attribute;
+
+
+ #strip off trailing comments
+ $feature_line =~ s/\#.*//;
+
+ my @chunks = split(/\t/, $feature_line);
+
+ %feature = (
+ 'seqid' => uri_unescape($chunks[0]),
+ 'source' => uri_unescape($chunks[1]),
+ 'type' => uri_unescape($chunks[2]),
+ 'start' => $chunks[3],
+ 'end' => $chunks[4],
+ 'score' => $chunks[5],
+ 'strand' => $strand_conversion{$chunks[6]},
+ 'phase' => $chunks[7]
+ );
+
+ if ($chunks[8]) {
my @attributes = split( /;/, $chunks[8] );
- my %attributes;
- foreach my $attribute (@attributes) {
- my ( $name, $value ) = split( /=/, $attribute );
- $name = uri_unescape($name);
- my @split_values = map { uri_unescape($_) } split(/,/, $value);
- if(scalar(@split_values) > 1) {
- $attributes{$name} = \@split_values;
- }
- else {
- $attributes{$name} = $split_values[0];
+ my %attributes;
+ foreach my $attribute (@attributes) {
+ my ( $name, $value ) = split( /=/, $attribute );
+ $name = uri_unescape($name);
+ my @split_values = map { uri_unescape($_) } split(/,/, $value);
+ if(scalar(@split_values) > 1) {
+ $attributes{$name} = \@split_values;
+ }
+ else {
+ $attributes{$name} = $split_values[0];
+ }
}
+ $feature{'attribute'} = \%attributes;
}
- $feature{'attribute'} = \%attributes;
- }
- return \%feature;
+ return \%feature;
}
-sub _read_line {
+=head2 parse_next_sequence
- my $self = shift;
- my $fh = $self->{'filehandle'};
+ Arg [1] : File handle
+ Description: Returns a hashref in the format -
+ {
+ header => scalar,
+ sequence => scalar,
+
+ }
+ Returntype : Hashref of a GFF3 sequence line
- my $line;
+=cut
+
+sub parse_next_sequence {
+
+ my $self = shift;
- if ( defined( $self->{'first_feature_line'} ) ) {
- $line = $self->{'first_feature_line'};
- $self->{'first_feature_line'} = undef;
- }
- else {
- $line = <$fh>;
- if ( defined($line) ) {
- chomp $line;
+ my $next_line;
+ my $sequence;
+ my $header;
+
+ while (($next_line = $self->_read_line() ) && defined($next_line) ) {
+
+ next if ($next_line =~ /^\#/ || $next_line =~ /^\s*$/ ||
+ $next_line =~ /^\/\//);
+
+ if ($next_line =~ /^>/) {
+ if ($header) {
+ #next fasta header encountered
+ $self->{'next_fasta_header'} = $next_line;
+ last;
+
+ } else {
+ $header = $next_line;
+ }
+ } else {
+ $sequence .= $next_line;
+ }
}
- }
- return $line;
+ return undef unless ($sequence || $header);
+
+ my %sequence = (header => $header , sequence => $sequence );
+
+ return \%sequence;
+}
+
+
+sub _read_line {
+
+ my $self = shift;
+ my $fh = $self->{'filehandle'};
+
+ my $line;
+
+ if (defined($self->{'first_non_header_line'})) {
+ $line = $self->{'first_non_header_line'};
+ $self->{'first_non_header_line'} = undef;
+ } elsif ( defined($self->{'next_fasta_header'} )) {
+ $line = $self->{'next_fasta_header'};
+ $self->{'next_fasta_header'} = undef;
+ }
+ else {
+ $line = <$fh>;
+ if (defined($line)) {
+ chomp $line;
+ if (!$line) {
+ #parse next line if current line is empty
+ $line = $self->_read_line();
+ }
+ }
+ }
+
+ return $line;
}
sub close {
- my $self = shift;
- $self->{"filehandle"} = undef;
+
+ my $self = shift;
+ $self->{"filehandle"} = undef;
+
}
1;