Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts/run-mummer1.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 # **SEVERELY** antiquated script for running the mummer 1 suite |
| jpayne@69 | 4 # -r option reverse complements the query sequence, coordinates of the reverse |
| jpayne@69 | 5 # matches will be relative to the reversed sequence |
| jpayne@69 | 6 # |
| jpayne@69 | 7 |
| jpayne@69 | 8 set ref = $1 |
| jpayne@69 | 9 set qry = $2 |
| jpayne@69 | 10 set pfx = $3 |
| jpayne@69 | 11 set rev = $4 |
| jpayne@69 | 12 |
| jpayne@69 | 13 set bindir = __BIN_DIR |
| jpayne@69 | 14 |
| jpayne@69 | 15 if($ref == '' || $qry == '' || $pfx == '') then |
| jpayne@69 | 16 echo "USAGE: $0 <fasta reference> <fasta query> <prefix> [-r]" |
| jpayne@69 | 17 exit(-1) |
| jpayne@69 | 18 endif |
| jpayne@69 | 19 |
| jpayne@69 | 20 echo "Find MUMs" |
| jpayne@69 | 21 $bindir/mummer -mum -l 20 $rev $ref $qry | tail +2 > $pfx.out |
| jpayne@69 | 22 echo "Determine gaps" |
| jpayne@69 | 23 $bindir/gaps $ref $rev < $pfx.out > $pfx.gaps |
| jpayne@69 | 24 echo "Align gaps" |
| jpayne@69 | 25 $bindir/annotate $pfx.gaps $qry > $pfx.align |
| jpayne@69 | 26 mv witherrors.gaps $pfx.errorsgaps |