#!/usr/bin/perl
#______________________________________________________________________
# Title     : B (for Bio) or bio_lib.pl
# Usage     : require "B.pl"; ##<-- This is very slow, so you'd better
#             copy the subroutines in your prog. or make a smaller lib files
#               which are classified according to functions(like, Bio_Seq.pl
#               for sequence handling, Bio_Array.pl for various array
#               subroutines..), or make your own module out of this, do whatever
#               you want....
#
#             To find out if there are any useful subroutines for you,
#              just search keywords like
#              'open_msf_files'
#                  while msf is a file format much used in multiple
#                  sequence handling
#              or  try  open_fasta_files
#
#              Then read carefully what they accept and return in the
#                information box in front of the subroutines.
#
# Function  : This has all the sub routines a biomatic has developed.
#             They are:
#               1) Very general programming level subroutines
#               2) Biological sequence handling level subroutines
#
#             You can copy any of the sub routines in this file, modify, use
#             in yours...
#             PLEASE MODIFY AS FREELY AS YOU WANT !!
#
#             " I am the programmer and I will try to debug with all my
#             efforts if you have any problems with my codes."
#
#             All my subroutines are tested in small files
#             If you want to have such single example program
#             to see how they really work, pls contact me( A Biomatic )
#             For example, a file called  'handle_arguments.pl' exists to
#             test the subroutine 'handle_arguments'. Usually you can find them
#             in  http://www.mrc-lmb.cam.ac.uk/genomes/jong/B.pl.html
#
#             This was meant to be used in Bioperl project, but I did not
#             have time to make object oriented module out of this. Also,
#             these procedural subroutines might be easier for a lot of
#             people.
#
# Example   : require "B.pl"; BUT, I recommand you take subroutines out and
#             use it directly or modify in your programs.
# Warning   : CopyLEFTed, for the enhancement of Biology, Biomatics, and Science.
#             This is a development companion, nothing else.
#             Class is for classification of my subroutines. If it is B, it can
#             be useful for biological sequence data handling. If it's Utility,
#             it can also be used for general purpose file handling stuff.
#             File, Array, Hash,... are my classification items.
# Keywords  : Biology, perl library, sequence handling lib
# Options   : nothing (used as subroutine library)
#             There are certain package structures;
#               1. Bio is the highest structure. This includes file handling
#                  and utility stuff, too.
#               2. Bio::Seq  is rather specific for sequence handling stuff.
#                  To be sorted and developed later.
#               3. YOU can add, modify or discuss on this structure anytime :-)
#
# Version   : 1.6    (Sept/21/1997)
#------------------------------------------------------------------