Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
Do not use this module directly. Use it via the Bio::SeqIO class.
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)
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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