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#!/usr/bin/perl
#
# run sim4 once for each line in the matchlist file
#
#
my @contigs = ();
system ("rm -f sim4.results");
while (<>) {
chomp;
@f = split /\t/, $_;
$estfilename = shift @f;
system ("echo '$estfilename' | cdbyank ~/galdieria/galdi3/Newbler_all_454AllContigs.fna.long.uc.cidx > mrna.fa");
system ("echo '@f' | cdbyank ~/galdieria/galdi3/build3.fa.cidx > genomic.fa");
system ("perl -i.orig -p -e 's/^Incorrectly.*fixed.\n//' mrna.fa genomic.fa");
system ("keepOnlyLonger.pl mrna.fa genomic.fa");
if (open(LONG, "<genomic.fa.long")) {
close LONG;
system ("echo '--------\n>$estfilename' >> sim4.results");
system ("sim4 mrna.fa genomic.fa.long >> sim4.results");
}
}
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