annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/run-mummer3 @ 69:33d812a61356

planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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jpayne@69 1 #! -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 = $3
jpayne@69 15
jpayne@69 16 set bindir = /mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23
jpayne@69 17
jpayne@69 18 if($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