Mercurial > repos > bgruening > jbrowse2
comparison convertMAF.sh @ 0:53c2be00bb6f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
| author | bgruening |
|---|---|
| date | Wed, 05 Jun 2024 08:15:49 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:53c2be00bb6f |
|---|---|
| 1 #!/usr/bin/env bash | |
| 2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh | |
| 3 # maf2bed modified to work right as a python script by ross lazarus in desperation | |
| 4 # MAF file must contain the species name and chromosome name | |
| 5 # e.g. hg38.chr1 in the sequence identifiers with hg38 passed in as $2 | |
| 6 python $3/maf2bed.py $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed | |
| 7 bgzip -c $4.sorted.bed > $4.sorted.bed.gz | |
| 8 tabix -p bed $4.sorted.bed.gz |