Mercurial > repos > bgruening > jbrowse2
diff 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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convertMAF.sh Wed Jun 05 08:15:49 2024 +0000 @@ -0,0 +1,8 @@ +#!/usr/bin/env bash +# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh +# maf2bed modified to work right as a python script by ross lazarus in desperation +# MAF file must contain the species name and chromosome name +# e.g. hg38.chr1 in the sequence identifiers with hg38 passed in as $2 +python $3/maf2bed.py $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed +bgzip -c $4.sorted.bed > $4.sorted.bed.gz +tabix -p bed $4.sorted.bed.gz