jpayne@69: #! -f
jpayne@69: #
jpayne@69: # **SEVERELY** antiquated script for running the mummer 1 suite
jpayne@69: # -r option reverse complements the query sequence, coordinates of the reverse
jpayne@69: # matches will be relative to the reversed sequence
jpayne@69: #
jpayne@69: 
jpayne@69: set ref = $1
jpayne@69: set qry = $2
jpayne@69: set pfx = $3
jpayne@69: set rev = $4
jpayne@69: 
jpayne@69: set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23
jpayne@69: 
jpayne@69: if($ref == '' || $qry == '' || $pfx == '') then
jpayne@69:     echo "USAGE: $0 <fasta reference> <fasta query> <prefix> [-r]"
jpayne@69:     exit(-1)
jpayne@69: endif
jpayne@69: 
jpayne@69: echo "Find MUMs"
jpayne@69: $bindir/mummer -mum -l 20 $rev $ref $qry | tail +2 > $pfx.out
jpayne@69: echo "Determine gaps"
jpayne@69: $bindir/gaps $ref $rev < $pfx.out > $pfx.gaps
jpayne@69: echo "Align gaps"
jpayne@69: $bindir/annotate $pfx.gaps $qry > $pfx.align
jpayne@69: mv witherrors.gaps $pfx.errorsgaps