Mercurial > repos > fubar > jbrowse2

comparison convertMAF.sh @ 57:94264fe60478 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
author fubar
date Thu, 21 Mar 2024 08:01:42 +0000
parents d78175596286
children e7a6f7a7148d
comparison
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56:c0097a584a8a 57:94264fe60478
1 #!/usr/bin/env bash 1 #!/usr/bin/env bash
2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh 2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
3 # MAF file must contain the species name and chromosome name 3 # MAF file must contain the species name and chromosome name
4 # e.g. hg38.chr1 in the sequence identifiers. 4 # e.g. hg38.chr1 in the sequence identifiers.
5 perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed 5 perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
6 bgzip $4.sorted.bed 6 bgzip -c $4.sorted.bed > $4.sorted.bed.gz
7 tabix -p bed $4.sorted.bed.gz 7 tabix -p bed $4.sorted.bed.gz