Mercurial > repos > fubar > jbrowse2

view convertMAF.sh @ 17:4c201a3d4755 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
author fubar
date Sun, 28 Jan 2024 06:48:52 +0000
parents d78175596286
children 94264fe60478
line wrap: on
line source

#!/usr/bin/env bash
# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
#  MAF file must contain the species name and chromosome name
#  e.g. hg38.chr1 in the sequence identifiers.
perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
bgzip $4.sorted.bed
tabix -p bed $4.sorted.bed.gz