Mercurial > repos > fubar > jbrowse2
view convertMAF.sh @ 98:b1260bca5fdc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
author | bgruening |
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date | Wed, 05 Jun 2024 10:00:07 +0000 |
parents | e7a6f7a7148d |
children |
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#!/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