Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_make_bam.py @ 35:259891fce7fd draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
author peterjc
date Wed, 09 Aug 2017 13:32:11 -0400
parents 0785a6537f3e
children cee8f9005e43
comparison
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34:0785a6537f3e 35:259891fce7fd
54 shutil.move(bam_stem + ".bam", bam_file) 54 shutil.move(bam_stem + ".bam", bam_file)
55 os.remove(bam_stem + ".bam.bai") # Let Galaxy handle that... 55 os.remove(bam_stem + ".bam.bai") # Let Galaxy handle that...
56 56
57 57
58 def make_bam(mira_convert, maf_file, fasta_file, bam_file, log_handle): 58 def make_bam(mira_convert, maf_file, fasta_file, bam_file, log_handle):
59 if not os.path.isfile(mira_convert):
60 return "Missing binary %r" % mira_convert
61 if not os.path.isfile(maf_file): 59 if not os.path.isfile(maf_file):
62 return "Missing input MIRA file: %r" % maf_file 60 return "Missing input MIRA file: %r" % maf_file
63 if not os.path.isfile(fasta_file): 61 if not os.path.isfile(fasta_file):
64 return "Missing padded FASTA file: %r" % fasta_file 62 return "Missing padded FASTA file: %r" % fasta_file
65 63