Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 25:172acf9c7a53 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 50ecae3ea703a1b04501cc44f0d1fa6d714a6cc9
author fubar
date Sat, 03 Feb 2024 22:07:55 +0000
parents fb6cc7bc24df
children 4ff1ed2065cc
comparison
equal deleted inserted replaced
24:fb6cc7bc24df 25:172acf9c7a53
457 if self.genome_name is None: 457 if self.genome_name is None:
458 self.genome_name = ( 458 self.genome_name = (
459 genome_name # first one for all tracks - other than paf 459 genome_name # first one for all tracks - other than paf
460 ) 460 )
461 self.genome_firstcontig = None 461 self.genome_firstcontig = None
462 fl = open(fapath, "r").readline().strip().split(">", 1) 462 fl = open(fapath, "r").readline().strip().split(">")
463 if len(fl) > 1: 463 if len(fl) > 1:
464 self.genome_firstcontig = fl[1].split().strip() 464 fl = fl[1]
465 if len(fl.split()) > 1:
466 self.genome_firstcontig = fl.split()[0].strip()
467 else:
468 self.genome_firstcontig = fl
465 if self.config_json.get("assemblies", None): 469 if self.config_json.get("assemblies", None):
466 self.config_json["assemblies"] += assemblies 470 self.config_json["assemblies"] += assemblies
467 else: 471 else:
468 self.config_json["assemblies"] = assemblies 472 self.config_json["assemblies"] = assemblies
469 473