#!/bin/bash
# Copyright (c) 2010, Elmar Pruesse <epruesse@mpi-bremen.de>
# All rights reserved.
# 
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#     * Redistributions of source code must retain the above copyright
#       notice, this list of conditions and the following disclaimer.
#     * Redistributions in binary form must reproduce the above copyright
#       notice, this list of conditions and the following disclaimer in the
#       documentation and/or other materials provided with the distribution.
#     * Neither the name of the <organization> nor the
#       names of its contributors may be used to endorse or promote products
#       derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

set -e

if [ -z "$1" ]; then
  echo "${0##*/} <filename> [size] [max]"
  echo "  Splits multi-fasta file <filename> into chunks of [size] sequences."
  echo "  If size is not specified, a default of 1000 is used."
  exit 1;
fi

FILENAME="$1"
if [ ! -r "$FILENAME" ]; then
  echo "Cannot read from file '$FILENAME'!"
  exit 2;
fi

FILEBASE=`basename $FILENAME`
PREFIX=${FILEBASE%.*}
SUFFIX=${FILEBASE#$PREFIX}

CHUNK="$2"
if [ -z "$CHUNK" ]; then
  CHUNK=1000
fi
if [ "$CHUNK" -lt 1 ]; then
  echo "Chunk size must be greater than one!"
  exit 3
fi

MAX="$3"
if [ -z "$MAX" ]; then
  MAX=99999999
fi

awk '
BEGIN {
  N=0; 
  ON=0; 
} 

/^>/ { 
  if (N % '$CHUNK' == 0) ++ON
  ++N
  if (N > '$MAX'*'$CHUNK') exit 0
} 

{
   print > "'"$PREFIX"'." ON "'"$SUFFIX"'"  
}
' $FILENAME