/usr/share/doc/infernal/examples/testsuite/itest3-msa-integrity.pl is in infernal 1.1.2-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 | #! /usr/bin/perl
# Look for any problems in cmalign/cmsearch that corrupt the input sequences.
#
# Usage: ./itest3-msa-integrity.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./itest3-msa-integrity.pl .. .. tmpfoo
#
# EPN, Fri Apr 27 14:45:16 2012
# HMMER3: i13-msa-integrity.pl [SRE, Tue Mar 9 09:19:22 2010 [Janelia]]
$builddir = shift;
$srcdir = shift;
$tmppfx = shift;
# Verify that we have all the executables we need for the test.
if (! -x "$builddir/src/cmalign") { die "FAIL: didn't find cmalign binary in $builddir/src"; }
if (! -x "$builddir/src/cmemit") { die "FAIL: didn't find cmemit binary in $builddir/src"; }
if (! -x "$builddir/src/cmsearch") { die "FAIL: didn't find cmsearch binary in $builddir/src"; }
if (! -x "$builddir/easel/miniapps/esl-reformat") { die "FAIL: didn't find esl-reformat binary in $builddir/easel/miniapps"; }
if (! -x "$builddir/easel/miniapps/esl-shuffle") { die "FAIL: didn't find esl-shuffle binary in $builddir/easel/miniapps"; }
# Verify that we have all the datafiles we need.
if (! -e "$srcdir/testsuite/tRNA.c.cm") { die "FAIL: didn't find tRNA.c.cm in $srcdir/testsuite"; }
$profile = "$srcdir/testsuite/tRNA.c.cm";
foreach $trial (1..5)
{
foreach $n (1, 10)
{
# homologous sequence fragments: generated from local profile
`$builddir/src/cmemit -o $tmppfx.fa -N $n $profile`;
if ($? != 0) { die "FAIL: cmemit"; }
&cmalign_msa_integrity_check ("$tmppfx.fa", $profile);
&cmsearch_msa_integrity_check("$tmppfx.fa", $profile);
# random sequences
`$builddir/easel/miniapps/esl-shuffle --rna -G -N $n -L 50 -o $tmppfx.fa`;
if ($? != 0) { die "FAIL: esl-shuffle"; }
&cmalign_msa_integrity_check ("$tmppfx.fa", $profile);
&cmsearch_msa_integrity_check("$tmppfx.fa", $profile);
}
}
print "ok\n";
unlink "$tmppfx.sto";
unlink <$tmppfx.fa*>;
unlink "$tmppfx.tbl";
unlink "$tmppfx.gdf";
exit 0;
sub cmalign_msa_integrity_check
{
my ($fafile, $cmfile) = @_;
`$builddir/src/cmalign -o $tmppfx.sto $cmfile $fafile > /dev/null 2>&1`;
if ($? != 0) { die "FAIL: cmalign failed"; }
`$builddir/easel/miniapps/esl-reformat -r -u fasta $tmppfx.sto > $tmppfx.fa1 2>/dev/null`;
if ($? != 0) { die "FAIL: first esl-reformat failed"; }
`$builddir/easel/miniapps/esl-reformat -r -u fasta $fafile > $tmppfx.fa2 2>/dev/null`;
if ($? != 0) { die "FAIL: second esl-reformat failed"; }
`diff -b $tmppfx.fa1 $tmppfx.fa2 > /dev/null 2>&1`;
if ($? != 0) { die "FAIL: cmalign alignment corrupted\n"; }
0;
}
sub cmsearch_msa_integrity_check
{
my ($fafile, $cmfile) = @_;
my $i;
# need report = include threshold to have same hits in .sto, .tbl
`$builddir/src/cmsearch -E 1 --incE 1 --tblout $tmppfx.tbl -A $tmppfx.sto $cmfile $fafile > /dev/null 2>&1`;
if ($? != 0) { die "FAIL: cmsearch failed"; }
$nlines = `cat $tmppfx.tbl | grep -v "^#" | wc -l`;
if ($nlines == 0) { return 0; }
`$builddir/easel/miniapps/esl-sfetch --index $fafile > /dev/null 2>&1`;
if ($? != 0) { die "FAIL: esl-sfetch --index failed"; }
`cat $tmppfx.tbl | grep -v "^#" | awk '{print \$1, \$8, \$9, \$1}' > $tmppfx.gdf`;
if ($? != 0) { die "FAIL: gdf table"; }
`$builddir/easel/miniapps/esl-sfetch -Cf $fafile $tmppfx.gdf > $tmppfx.fa3`;
if ($? != 0) { die "FAIL: esl-sfetch failed"; }
# Grep out name/desc lines because they'll differ: esl-sfetch adds descline.
`$builddir/easel/miniapps/esl-reformat -r -u fasta $tmppfx.sto | grep -v "^>" > $tmppfx.fa1 2>/dev/null`;
if ($? != 0) { die "FAIL: first esl-reformat failed"; }
`$builddir/easel/miniapps/esl-reformat -r -u fasta $tmppfx.fa3 | grep -v "^>" > $tmppfx.fa2 2>/dev/null`;
if ($? != 0) { die "FAIL: second esl-reformat failed"; }
`diff -b $tmppfx.fa1 $tmppfx.fa2 > /dev/null 2>&1`;
if ($? != 0) { die "FAIL: cmsearch alignment corrupted"; }
0;
}
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