Mercurial > repos > iuc > jbrowse

comparison jbrowse.py @ 34:9de82b4963e6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
author iuc
date Wed, 11 Sep 2019 09:40:36 -0400
parents 0ae74c70b267
children 17359b808b01
comparison
equal deleted inserted replaced
33:0ae74c70b267 34:9de82b4963e6
652 652
653 def _sort_bed(self, data, dest): 653 def _sort_bed(self, data, dest):
654 # Only index if not already done 654 # Only index if not already done
655 if not os.path.exists(dest): 655 if not os.path.exists(dest):
656 cmd = ['sort', '-k1,1', '-k2,2n', data] 656 cmd = ['sort', '-k1,1', '-k2,2n', data]
657 self.subprocess_check_call(cmd, output=dest) 657 with open(dest, 'w') as handle:
658 self.subprocess_check_call(cmd, output=handle)
658 659
659 self.subprocess_check_call(['bgzip', '-f', dest]) 660 self.subprocess_check_call(['bgzip', '-f', dest])
660 self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz']) 661 self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz'])
661 662
662 def add_gff(self, data, format, trackData, gffOpts, **kwargs): 663 def add_gff(self, data, format, trackData, gffOpts, **kwargs):