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Commit b8c8c969 authored by Kieron Taylor's avatar Kieron Taylor :angry:
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Zapped icky \t characters

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modules/Bio/EnsEMBL/Utils/IO/GFFParser.pm
+ 72
− 72
View file @ b8c8c969
......@@ -40,16 +40,16 @@ 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) {
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 = $parser->parse_next_feature();
......@@ -134,23 +134,23 @@ sub parse_header {
my @header_lines;
while (($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 $1. GFFParser may return unexpected results as it is designed to parse GFF3 formatted files.");
}
}
}
#stop parsing features if ##FASTA directive encountered
last if ($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)) {
$self->{'first_non_header_line'} = $next_line;
$self->{'first_non_header_line'} = $next_line;
}
return \@header_lines;
......@@ -171,7 +171,7 @@ sub parse_header {
phase => scalar,
attribute => hashref,
}
}
Returntype : Hashref of a GFF3 feature line
=cut
......@@ -185,15 +185,15 @@ sub parse_next_feature {
while (($next_line = $self->_read_line() ) && defined($next_line) ) {
#stop parsing features if ##FASTA directive
last if ($next_line =~ /\#\#FASTA/);
next if ($next_line =~ /^\#/ || $next_line =~ /^\s*$/ ||
$next_line =~ /^\/\//);
$feature_line = $next_line;
last;
#stop parsing features if ##FASTA directive
last if ($next_line =~ /\#\#FASTA/);
next if ($next_line =~ /^\#/ || $next_line =~ /^\s*$/ ||
$next_line =~ /^\/\//);
$feature_line = $next_line;
last;
}
return undef unless $feature_line;
......@@ -204,20 +204,20 @@ sub parse_next_feature {
#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' => $chunks[7]
'seqid' => uri_unescape($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( /;/, $chunks[8] );
my %attributes;
......@@ -246,7 +246,7 @@ sub parse_next_feature {
header => scalar,
sequence => scalar,
}
}
Returntype : Hashref of a GFF3 sequence line
=cut
......@@ -261,21 +261,21 @@ sub parse_next_sequence {
while (($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 .= $next_line;
}
next if ($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 .= $next_line;
}
}
return undef unless ($sequence || $header);
......@@ -294,21 +294,21 @@ sub _read_line {
my $line;
if (defined($self->{'first_non_header_line'})) {
$line = $self->{'first_non_header_line'};
$self->{'first_non_header_line'} = undef;
$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;
$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();
}
}
$line = <$fh>;
if (defined($line)) {
chomp $line;
if (!$line) {
#parse next line if current line is empty
$line = $self->_read_line();
}
}
}
return $line;
......
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