#!/usr/local/bin/perl -w
#	Kevin Karplus
#	24 May 2002

# make_undertaker_alignment_list < target-many_alignments.html
#	> target-undertaker-align.script
# generates a script for undertaker to use the top alignments as
# sources for specific fragments and alignments.
#
# The script is NOT a complete undertaker script---it contains only
# the ReadFragmentAlignment commands to read in the a2m files.
# Setting up the target, selecting the training chains to use for 
# a generic fragment library, selecting a clash definition, ...
# all must be done first, before doing an Include command to read
# in the fragments.

# BUGS:
#	no usage message, almost no error checking.


$_=<STDIN>;
die "Header missing\n" if ! /Template/;
<STDIN>;

while (<STDIN>)
{
    @cols = split(/\t/);
    print "ReadFragmentAlignment $cols[1]\n";
}