Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/exact-tandems @ 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 #! -f |
| jpayne@69 | 2 # |
| jpayne@69 | 3 # Find exact tandem repeats in specified file involving an |
| jpayne@69 | 4 # exact duplicate of at least the specified length |
| jpayne@69 | 5 |
| jpayne@69 | 6 set filename = $1 |
| jpayne@69 | 7 set matchlen = $2 |
| jpayne@69 | 8 |
| jpayne@69 | 9 set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23 |
| jpayne@69 | 10 set scriptdir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts |
| jpayne@69 | 11 |
| jpayne@69 | 12 if ($filename == '' || $matchlen == '') then |
| jpayne@69 | 13 echo "USAGE: $0 <file> <min-match-len>" |
| jpayne@69 | 14 exit -1 |
| jpayne@69 | 15 endif |
| jpayne@69 | 16 |
| jpayne@69 | 17 echo "Finding matches" |
| jpayne@69 | 18 $bindir/repeat-match -t -n $matchlen $filename | tail +3 > $$.tmp.matches |
| jpayne@69 | 19 if ($status != 0) exit -1 |
| jpayne@69 | 20 |
| jpayne@69 | 21 echo "Tandem repeats" |
| jpayne@69 | 22 sort -k1n -k2n $$.tmp.matches | awk -f $scriptdir/tandem-repeat.awk |
| jpayne@69 | 23 rm -f $$.tmp.matches |