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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/exact-tandems @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #! -f
2 #
3 # Find exact tandem repeats in specified file involving an
4 # exact duplicate of at least the specified length
5
6 set filename = $1
7 set matchlen = $2
8
9 set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23
10 set scriptdir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts
11
12 if ($filename == '' || $matchlen == '') then
13 echo "USAGE: $0 <file> <min-match-len>"
14 exit -1
15 endif
16
17 echo "Finding matches"
18 $bindir/repeat-match -t -n $matchlen $filename | tail +3 > $$.tmp.matches
19 if ($status != 0) exit -1
20
21 echo "Tandem repeats"
22 sort -k1n -k2n $$.tmp.matches | awk -f $scriptdir/tandem-repeat.awk
23 rm -f $$.tmp.matches