Bio::SeqIO::tab - nearly raw sequence file input/output

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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

DESCRIPTION

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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)

FEEDBACK

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Mailing Lists

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

Support

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.

Reporting Bugs

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/

AUTHORS

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

APPENDIX

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

next_seq

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

write_seq

 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
BioPerl documentation Contained in the BioPerl distribution. 
#-----------------------------------------------------------------------------
# PACKAGE : Bio::SeqIO::tab
# AUTHOR  : Philip Lijnzaad <p.lijnzaad@med.uu.nl>
# CREATED : Feb 6 2003
#
# Copyright (c) This module is free software; you can redistribute it
# and/or modify it under the same terms as Perl itself.
#
# _History_
#
# Ewan Birney <birney@ebi.ac.uk> developed the SeqIO
# schema and the first prototype modules.
#
# This code is based on his Bio::SeqIO::raw
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...

package Bio::SeqIO::tab;
use strict;

use Bio::Seq;

use base qw(Bio::SeqIO);


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/\W//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;