jpayne@69: #! -f
jpayne@69: #
jpayne@69: # for running the basic mummer 3 suite, should use nucmer instead when possible
jpayne@69: # to avoid the confusing reverse coordinate system of the raw programs.
jpayne@69: #
jpayne@69: # NOTE:  be warned that all reverse matches will then
jpayne@69: # be relative to the reverse complement of the query sequence.
jpayne@69: #
jpayne@69: # Edit this script as necessary to alter the matching and clustering values
jpayne@69: #
jpayne@69: 
jpayne@69: set ref = $1
jpayne@69: set qry = $2
jpayne@69: set pfx = $3
jpayne@69: 
jpayne@69: set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23
jpayne@69: 
jpayne@69: if($ref == '' || $qry == '' || $pfx == '') then
jpayne@69:     echo "USAGE: $0 <fasta reference> <multi-fasta query> <prefix>"
jpayne@69:     exit(-1)
jpayne@69: endif
jpayne@69: 
jpayne@69: echo "Find MUMs"
jpayne@69: $bindir/mummer -mumreference -b -l 20 $ref $qry > $pfx.out
jpayne@69: echo "Determine gaps"
jpayne@69: $bindir/mgaps -l 100 -f .12 -s 600 < $pfx.out > $pfx.gaps
jpayne@69: echo "Align gaps"
jpayne@69: $bindir/combineMUMs -x -e .10 -W $pfx.errorsgaps $ref $qry $pfx.gaps > $pfx.align