view convertMAF.sh @ 112:56f9a6e0fe80 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
author bgruening
date Thu, 04 Jul 2024 08:40:21 +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