Mercurial > repos > fubar > jbrowse2

comparison convertMAF.sh @ 61:e7a6f7a7148d draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
author fubar
date Tue, 26 Mar 2024 00:52:34 +0000
parents 94264fe60478
children
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60:81d535970196 61:e7a6f7a7148d
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 # maf2bed modified to work right as a python script by ross lazarus in desperation
3 # MAF file must contain the species name and chromosome name 4 # MAF file must contain the species name and chromosome name
4 # e.g. hg38.chr1 in the sequence identifiers. 5 # e.g. hg38.chr1 in the sequence identifiers with hg38 passed in as $2
5 perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed 6 python $3/maf2bed.py $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
6 bgzip -c $4.sorted.bed > $4.sorted.bed.gz 7 bgzip -c $4.sorted.bed > $4.sorted.bed.gz
7 tabix -p bed $4.sorted.bed.gz 8 tabix -p bed $4.sorted.bed.gz