/usr/bin/run-mummer1 is in mummer 3.23~dfsg-3.
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 | #!/bin/sh -e
#
# **SEVERELY** antiquated script for running the mummer 1 suite
# -r option reverse complements the query sequence, coordinates of the reverse
# matches will be relative to the reversed sequence
#
usage () {
echo "Usage: `basename $0` <fasta reference> <fasta query> <prefix> [-r]"
return 67 # EX_USAGE
}
if [ $# -ne 3 -a $# -ne 4 ] ; then
echo "You provided $# arguments."
usage
fi
ref="$1"
qry="$2"
pfx="$3"
rev="$4"
bindir=/usr/bin
if [ ! -e "$ref" ] ; then
echo "File for fasta reference $ref does not exist."
usage
fi
if [ ! -e "$qry" ] ; then
echo "File for fasta query $qry does not exist."
usage
fi
if [ "$pfx" = "" ] ; then
usage
fi
echo "Find MUMs"
$bindir/mummer -mum -l 20 "$rev" "$ref" "$qry" | tail +2 > "$pfx".out
echo "Determine gaps"
$bindir/gaps "$ref" "$rev" < "$pfx".out > "$pfx".gaps
echo "Align gaps"
$bindir/mummer-annotate "$pfx".gaps "$qry" > "$pfx".align
mv witherrors.gaps "$pfx".errorsgaps
|