bio::seqio::tab(3pm) [debian man page]

Bio::SeqIO::tab(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::tab(3pm)

NAME

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

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)

FEEDBACK

   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

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

APPENDIX

       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

perl v5.14.2							    2012-03-02						      Bio::SeqIO::tab(3pm)