Mercurial > repos > fubar > jbrowse2
comparison convertMAF.sh @ 0:d78175596286 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
| author | fubar |
|---|---|
| date | Mon, 08 Jan 2024 09:20:33 +0000 |
| parents | |
| children | 94264fe60478 |
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| -1:000000000000 | 0:d78175596286 |
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| 1 #!/usr/bin/env bash | |
| 2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh | |
| 3 # MAF file must contain the species name and chromosome name | |
| 4 # e.g. hg38.chr1 in the sequence identifiers. | |
| 5 perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed | |
| 6 bgzip $4.sorted.bed | |
| 7 tabix -p bed $4.sorted.bed.gz |