Mercurial > repos > fubar > jbrowse2
diff convertMAF.sh @ 61:e7a6f7a7148d draft
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 |
line wrap: on
line diff
--- a/convertMAF.sh Mon Mar 25 02:10:05 2024 +0000 +++ b/convertMAF.sh Tue Mar 26 00:52:34 2024 +0000 @@ -1,7 +1,8 @@ #!/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. -perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed +# 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