#!/bin/bash
#
# Performs a local alignment on two sequences passed
# from the command line.
#
# Example:
#
#     global-align.sh THISLINE ISALIGNED -gapopen 1
#     global-align.sh THISLINE ISALIGNED -data BLOSUM30
#
# The code also works if both entries are files.
#
#     global-align.sh file1.fa file2.fa  -gapopen 1
#     global-align.sh file1.fa file2.fa  -data BLOSUM30
#
# If the first parameter is a file name, run in file mode.
# otherwise turns shell parameters into input streams as shown by
# Brad Pedersen in https://www.biostars.org/p/100676/#100689
#
# Read more on parameters at: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needle.html
#
# Replace the tool 'needle' with the tool named 'stretcher'
# for a less rigorous but better performing algorithm.
#
# We use needle since it formats the output more nicely than strecher.
#
ALIGNER=needle

# Uncomment this line for higher performance.
# ALIGNER=strecher

# Run in strict mode.
set -ue

# All additional  parameters past the first two are passed down via  ${@:3}
if [ -f $1 ];
then
	$ALIGNER $1 $2 "${@:3}" -filter
else

	$ALIGNER <(echo -e ">a\n$1") <(echo -e ">b\n$2") "${@:3}" -filter
fi