Mercurial > repos > rliterman > csp2
comparison 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 |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!__CSH_PATH -f | |
| 2 # | |
| 3 # for running the basic mummer 3 suite, should use nucmer instead when possible | |
| 4 # to avoid the confusing reverse coordinate system of the raw programs. | |
| 5 # | |
| 6 # NOTE: be warned that all reverse matches will then | |
| 7 # be relative to the reverse complement of the query sequence. | |
| 8 # | |
| 9 # Edit this script as necessary to alter the matching and clustering values | |
| 10 # | |
| 11 | |
| 12 set ref = $1 | |
| 13 set qry = $2 | |
| 14 set pfx = $3 | |
| 15 | |
| 16 set bindir = __BIN_DIR | |
| 17 | |
| 18 if($ref == '' || $qry == '' || $pfx == '') then | |
| 19 echo "USAGE: $0 <fasta reference> <multi-fasta query> <prefix>" | |
| 20 exit(-1) | |
| 21 endif | |
| 22 | |
| 23 echo "Find MUMs" | |
| 24 $bindir/mummer -mumreference -b -l 20 $ref $qry > $pfx.out | |
| 25 echo "Determine gaps" | |
| 26 $bindir/mgaps -l 100 -f .12 -s 600 < $pfx.out > $pfx.gaps | |
| 27 echo "Align gaps" | |
| 28 $bindir/combineMUMs -x -e .10 -W $pfx.errorsgaps $ref $qry $pfx.gaps > $pfx.align |