/usr/share/doc/infernal/examples/testsuite/bug-i28.pl is in infernal 1.1.2-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | #! /usr/bin/perl
# bug i28 - Incomplete CP9Bands cloning.
#
# EPN, Wed Jul 18 06:12:48 2012
#
# The CP9Bands_t object (cm->cp9b) was not being completely cloned in
# hmmband.c:cp9_CloneBands(). In particular the {J,L,R,T}valid arrays
# for truncated alignment were not being cloned. This caused a potential
# problem when a single envelope in a truncated pass included more
# than 1 hit (the only time the cloned bands are used) if the required
# matrix was near the maximum allowed size.
#
# The instance here is the only case I've ever seen. It's very rare
# because it requires multiple hits in a single truncated envelope
# and truncated envelopes can only occur in the first/final W residues
# of a sequence.
#
# See BUGTRAX i28 description for more information.
#
# bug-i28.cm - SRP CM built from the 'seed' alignment used in
# Menzel, P., Gorodkin, J., & Stadler, P. F. (2009).
# The tedious task of finding homologous noncoding
# RNA genes. RNA (New York, NY), 15(12), 2075–2082. doi:10.1261/rna.1556009
#
# bug-i28.fa - the final 373 residues of a single sequence from the
# ENSEMBL release 47 genome of Macaca mulatta (Rhesus macaque).
# This genome was searched in the Stadler paper.
$usage = "perl bug-i28.pl <cmsearch> <path to bug-i28.cm> <path to bug-i28.fa>\n";
if ($#ARGV != 2) { die "Wrong argument number.\n$usage"; }
$cmsearch = shift;
$cmfile = shift;
$seqfile = shift;
$ok = 1;
if ($ok) {
system("$cmsearch $cmfile $seqfile > /dev/null 2> /dev/null");
if ($? != 0) { $ok = 0; }
}
if ($ok) { print "ok\n"; exit 0; }
else { print "FAILED\n"; exit 1; }
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