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Summary

Bio::SeqIO::tab - nearly raw sequence file input/output
stream. Reads/writes id"\t"sequence"\n"

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

Do not use this module directly. Use it via the Bio::SeqIO class.

Description

This object can transform Bio::Seq objects to and from tabbed flat
file databases.
It is very useful when doing large scale stuff using the Unix command
line utilities (grep, sort, awk, sed, split, you name it). Imagine
that you have a format converter 'seqconvert' along the following
lines:

  my $in  = Bio::SeqIO->newFh(-fh => \*STDIN , '-format' => $from);
  my $out = Bio::SeqIO->newFh(-fh=> \*STDOUT, '-format' => $to);
  print $out $_ while <$in>;

then you can very easily filter sequence files for duplicates as:

  $ seqconvert < foo.fa -from fasta -to tab | sort -u |\
       seqconvert -from tab -to fasta > foo-unique.fa

Or grep [-v] for certain sequences with:

  $ seqconvert < foo.fa -from fasta -to tab | grep -v '^S[a-z]*control' |\
       seqconvert -from tab -to fasta > foo-without-controls.fa

Or chop up a huge file with sequences into smaller chunks with:

  $ seqconvert < all.fa -from fasta -to tab | split -l 10 - chunk-
  $ for i in chunk-*; do seqconvert -from tab -to fasta < $i > $i.fa; done
  # (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing 10
  # sequences)

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq object

Methods code

sub next_seq {

   my ($self,@args) = @_;
   ## When its 1 sequence per line with no formatting at all,
   ## grabbing it should be easy :)

   my $nextline = $self->_readline();
   chomp($nextline) if defined $nextline;
   return unless defined $nextline;
   if ($nextline =~ /^([^\t]*)\t(.*)/) {
       my ($id, $seq)=($1, uc($2));
       $seq =~ s/\s+//g;
       return  Bio::Seq->new(-display_id=> $id, -seq => $seq);
   }  else {
       $self->throw("Can't parse tabbed sequence entry:'$nextline' around line $.");
   }

}

sub write_seq {

   my ($self,@seq) = @_;
   foreach (@seq) {
       if ($_->display_id() =~ /\t/) {
           $self->throw("display_id [".$_->display_id()."] contains TAB -- illegal in tab format");
       }
       $self->_print($_->display_id(), "\t",$_->seq, "\n") or return;
   }

   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return 1;
}

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

Philip Lijnzaad, p.lijnzaad@med.uu.nl

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _