Mercurial > repos > fubar > jbrowse2dev

comparison jbrowse2/jbrowse2.py @ 9:6a41f87b5d7f draft

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author fubar
date Fri, 05 Jan 2024 05:06:21 +0000
parents 1e6128ccc82b
children 0db895a99532
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8:1e6128ccc82b 9:6a41f87b5d7f
170 def process_genomes(self): 170 def process_genomes(self):
171 assemblies = [] 171 assemblies = []
172 for i, genome_node in enumerate(self.genome_paths): 172 for i, genome_node in enumerate(self.genome_paths):
173 if self.debug: 173 if self.debug:
174 log.info("genome_node=%s" % str(genome_node)) 174 log.info("genome_node=%s" % str(genome_node))
175 genome_name = genome_node["meta"]["dataset_dname"] 175 genome_name = genome_node["meta"]["dataset_dname"].strip().split()[0]
176 fapath = genome_node["path"] 176 fapath = genome_node["path"]
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,