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

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

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://github.com/bioperl/bioperl-live/issues

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 v5.32.1			  2019-12-07		    Bio::SeqIO::tab(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS | APPENDIX

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