NAME

Bio::Gonzales::Feat::IO::GFF3 - read and write gff files

SYNOPSIS

use Bio::Gonzales::Feat::IO::GFF3;

my $output = Bio::Gonzales::Feat::IO::GFF3->new( file => 'a.gff', mode => '>', escape_whitespace => 1 );
my $gffin = Bio::Gonzales::Feat::IO::GFF3->new( file => 'a.gff' );

# gzipped files can be read directly.
my $gffin = Bio::Gonzales::Feat::IO::GFF3->new( file => 'a.gff.gz' );

my $gffin = Bio::Gonzales::Feat::IO::GFF3->new('a.gff');

while ( my $feat = $gffin->next_feat ) {
  # $feat is a Bio::Gonzales::Feat
  next if ( $feat->type ne 'mRNA' );

  say STDERR $feat->id . " - " . $feat->parent_id;
}

$gffin->close;

DESCRIPTION

OPTIONS

mode => $mode

Bio::Gonzales::Feat::IO::GFF3 supports 3 different modes,

Bio::Gonzales::Feat::IO::GFF3->new(mode => '>', ...); #output
Bio::Gonzales::Feat::IO::GFF3->new(mode => '<', ...); #input, DEFAULT
Bio::Gonzales::Feat::IO::GFF3->new(mode => '>>', ...); #append

all modes also work with gzipped files (ending on '.gz').

fh => $fh

Bio::Gonzales::Feat::IO::GFF3 uses $fh to read or write data.

open my $fh, '<', 'file.gff3' or confess "Can't open filehandle: $!";
my $gff = Bio::Gonzales::Feat::IO::GFF3->new(fh => $fh, ...);

# ... do something ...

$gff->close;
close $fh;

file => $file

read from or write to the file $file

escape_whitespace => 1

Usually, only whitespaces in the Target attribute are escaped. If this feature is turned on, whitespace in all attribute values will be escaped.

record_filter => sub { ... }

Before reading in the GFF3 information, filter the raw line content according to the supplied function. This functionality is handy for big gff3 files where only a part of the output should be parsed.

Example:

my $sub = sub {
  my $line = shift;

  return $line =~ /\tmRNA\t/;
};
my $gff = Bio::Gonzales::Feat::IO::GFF3->new( file => '...', mode => '<', record_filter => $sub );

# ... only lines with the type 'mRNA' will be parsed ...

$gff->close;

METHODS

$gffio->write_feat($feat)

Write the feature to the output. Do not forget to call $gffio-close> at the end of the processing, otherwise you probably end up writing only half of the features.

my $feat = $gffio->next_feat()

Retrieve the next feature, if in reading mode.

$gffio->segments

$gffio->pragmas

$gffio->preprocess(\&process)

Change the gff input before the feature object gets instantiated. Arguments of the &process sub are the nine columns of the gff file split into an array.

Example sub: sub process { my @cols = @_;

    $cols[1] = "createdbyme";
    return @cols;
}

$gffio->comments

SEE ALSO

AUTHOR

jw bargsten, <joachim.bargsten at wur.nl>