Mercurial > repos > fubar > jbrowse2

annotate convertMAF.sh @ 78:7bb6259ea52f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
author fubar
date Mon, 01 Apr 2024 05:40:29 +0000
parents e7a6f7a7148d
children
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d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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1 #!/usr/bin/env bash
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
fubar
parents: 57
diff changeset
3 # maf2bed modified to work right as a python script by ross lazarus in desperation
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d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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4 # MAF file must contain the species name and chromosome name
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
fubar
parents: 57
diff changeset
5 # e.g. hg38.chr1 in the sequence identifiers with hg38 passed in as $2
e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
fubar
parents: 57
diff changeset
6 python $3/maf2bed.py $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
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94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 0
diff changeset
7 bgzip -c $4.sorted.bed > $4.sorted.bed.gz
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d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
8 tabix -p bed $4.sorted.bed.gz