#!/usr/bin/perl -w
# shortenName.pl
# shorten the sequence names to accession numbers from fasta file.

# Copyright 2013, Naoki Takebayashi <ntakebayashi@alaska.edu>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.

# Version: 20130612

while (<>){
    chomp;
    unless (/^>/) {  # Not the name line
       print "$_\n";
       next;
    }

    # We are dealing with the name when the process reaches here.
    s/^>\s*//;      # get rid of '>'

    my @line = split /\s+/;

    my $first = shift (@line);  # gi|49188826|gb|CO267808.1|CO267808
    my @numbers = split /\|/, $first;

    $accNum = $numbers[3];
    $accNum =~ s/\.\d+$//;  # remove version numbers

    print ">$accNum\n";
}