Ubuntu Manpages

Bio::DB::HTS::Kseq

Bindings to Kseq

Bio::DB::HTS::Kseq - Bindings to Kseq

Bindings to the Kseq library for iterating through a locally held FASTA/FASTQ file very quickly. Supports compressed and uncompressed files alongside filehandles.

  my $kseq = Bio::DB::HTS::Kseq->new('path/to/file');
  my $iter = $kseq->iterator();
  while(my $r = $iter->next_seq()) {
    say $r->name;
    say $r->desc;
    say $r->seq;
    say $r->qual;
  }
  # Allowing the object to go out of scope will close down all file handles

METHODS

"new"
  my $kseq = Bio::DB::HTS::Kseq->new('path/to/file');

Returns an instance of this object from a file path.

"newfh"
  open my $fh, '<', 'path' or die "Cannot open path: $!";
  binmode $fh;
  my $kseq = Bio::DB::HTS::Kseq->newfh($fh);

Returns an instance of this object from an opened file handle. This supports any known Perl glob/filehandle type

"iterator"
  my $iter = $kseq->iterator();

Returns the kseq iterator object