Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts/run-mummer3.csh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!__CSH_PATH -f |
| jpayne@69 | 2 # |
| jpayne@69 | 3 # for running the basic mummer 3 suite, should use nucmer instead when possible |
| jpayne@69 | 4 # to avoid the confusing reverse coordinate system of the raw programs. |
| jpayne@69 | 5 # |
| jpayne@69 | 6 # NOTE: be warned that all reverse matches will then |
| jpayne@69 | 7 # be relative to the reverse complement of the query sequence. |
| jpayne@69 | 8 # |
| jpayne@69 | 9 # Edit this script as necessary to alter the matching and clustering values |
| jpayne@69 | 10 # |
| jpayne@69 | 11 |
| jpayne@69 | 12 set ref = $1 |
| jpayne@69 | 13 set qry = $2 |
| jpayne@69 | 14 set pfx = $3 |
| jpayne@69 | 15 |
| jpayne@69 | 16 set bindir = __BIN_DIR |
| jpayne@69 | 17 |
| jpayne@69 | 18 if($ref == '' || $qry == '' || $pfx == '') then |
| jpayne@69 | 19 echo "USAGE: $0 <fasta reference> <multi-fasta query> <prefix>" |
| jpayne@69 | 20 exit(-1) |
| jpayne@69 | 21 endif |
| jpayne@69 | 22 |
| jpayne@69 | 23 echo "Find MUMs" |
| jpayne@69 | 24 $bindir/mummer -mumreference -b -l 20 $ref $qry > $pfx.out |
| jpayne@69 | 25 echo "Determine gaps" |
| jpayne@69 | 26 $bindir/mgaps -l 100 -f .12 -s 600 < $pfx.out > $pfx.gaps |
| jpayne@69 | 27 echo "Align gaps" |
| jpayne@69 | 28 $bindir/combineMUMs -x -e .10 -W $pfx.errorsgaps $ref $qry $pfx.gaps > $pfx.align |