Mercurial > repos > fubar > jbrowse2dev

annotate jbrowse2/convertMAF.sh @ 9:6a41f87b5d7f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Fri, 05 Jan 2024 05:06:21 +0000
parents cd5d63cd0eb5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cd5d63cd0eb5 Uploaded
fubar
parents:
diff changeset
1 #!/usr/bin/env bash
cd5d63cd0eb5 Uploaded
fubar
parents:
diff changeset
2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
cd5d63cd0eb5 Uploaded
fubar
parents:
diff changeset
3 # MAF file must contain the species name and chromosome name
cd5d63cd0eb5 Uploaded
fubar
parents:
diff changeset
4 # e.g. hg38.chr1 in the sequence identifiers.
cd5d63cd0eb5 Uploaded
fubar
parents:
diff changeset
5 perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
cd5d63cd0eb5 Uploaded
fubar
parents:
diff changeset
6 bgzip $4.sorted.bed
cd5d63cd0eb5 Uploaded
fubar
parents:
diff changeset
7 tabix -p bed $4.sorted.bed.gz