BTLib

Section: User Contributed Perl Documentation (3)
Updated: 2006-10-24
Index

NAME

BTLib - Perl extension for a Biology Toolkit Library.

SYNOPSIS

  use BTLib;

  Object creation:  new

  Component access:  seq  seq (sequence)  seqHead  seqHead (fasta_header)  seqFile  seqFile (filename)  killFile  killFile (boolean)  type  type (DNA or protein)

  Methods:  filterSeq (command)

  Internal methods:  DESTROY  seqToFile  fileToSeq

DESCRIPTION

BTLib offers an interface to apply various tools (like blast, the FDFor the pftools) to analyze a protein or DNA sequence.

The basic concept is that a sequence to analyze is represented by anobject of type BTLib. You create this object using the method new().The newly created objects has all its fields set to undefined. Forexample:
$main::seq = BTLib->new;

The next step is to provide a sequence to the new object. This can bedone in two ways: either provide the name of a file containing a FASTAformatted sequence using the method seqFile(), or provide the sequenceheader and the sequence itself using the methods seqHead() and seq()respectively. So we have either:
$main::seq->seqFile(``/tmp/my.seq'');

or:
$main::seq->seqHead(``>emb|AB000095|AB000095 ...'');
$main::seq->seq(``CGGCCGAGCCCAGCTCTCCGAG...'');

The sequence can be filtered, using an arbitrary Unix command thatwrites its results to standard output, using the method filterSeq().This generates a new sequence object. Thus you can say:
my $filteredSeq = $main::seq->filterSeq(``xnu'');

If you no longer need the original sequence, you can also write:
$main::seq = $main::seq->filterSeq(``xnu'');

The object takes care (automagicaly) of creating a temporary FASTAfile containing the sequence, if needed. The file is deleted when theobject dies. When a file is supplied to the object, it will not bedeleted, unless you call the killFile() method with a non-zeroparameter.

AUTHOR

Christian Iseli, LICR ITO, Christian.IseliAATTlicr.org