Mercurial > repos > fubar > jbrowse2dev

comparison jbrowse2/jbrowse2.py @ 8:1e6128ccc82b 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 04:57:29 +0000
parents 234cf4490901
children 6a41f87b5d7f
comparison
equal deleted inserted replaced
7:234cf4490901 8:1e6128ccc82b
177 faname = genome_name + ".fa.gz" 177 faname = genome_name + ".fa.gz"
178 fadest = os.path.realpath(os.path.join(self.outdir, faname)) 178 fadest = os.path.realpath(os.path.join(self.outdir, faname))
179 cmd = "bgzip -i -c %s > %s && samtools faidx %s" % ( 179 cmd = "bgzip -i -c %s > %s && samtools faidx %s" % (
180 fapath, 180 fapath,
181 fadest, 181 fadest,
182 fadest, 182 fadest
183 ) 183 )
184 log.info("### cmd = %s" % ' '.join(cmd))
184 self.subprocess_popen(cmd) 185 self.subprocess_popen(cmd)
185 adapter = { 186 adapter = {
186 "type": "BgzipFastaAdapter", 187 "type": "BgzipFastaAdapter",
187 "fastaLocation": { 188 "fastaLocation": {
188 "uri": faname, 189 "uri": faname,