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comparison macs21_wrapper.py @ 7:0c6b14f3fefc draft

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Attempt to fix installation of tool dependencies for UCSC/bigwig generation, and trap for undefined genome build.
author pjbriggs
date Tue, 21 Apr 2015 08:29:16 -0400
parents 15889783e759
children 78c15c0a96ae
comparison
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6:344dd37d1704 7:0c6b14f3fefc
75 # Check for chromosome sizes 75 # Check for chromosome sizes
76 if not os.path.exists(chrom_sizes): 76 if not os.path.exists(chrom_sizes):
77 # Determine genome build 77 # Determine genome build
78 chrom_sizes = os.path.basename(chrom_sizes) 78 chrom_sizes = os.path.basename(chrom_sizes)
79 genome_build = chrom_sizes.split('.')[0] 79 genome_build = chrom_sizes.split('.')[0]
80 if genome_build == '?':
81 # No genome build set
82 sys.stderr.write("ERROR genome build not set, cannot get sizes for '?'\n")
83 sys.exit(1)
80 print "Missing chrom sizes file, attempting to fetch for '%s'" % genome_build 84 print "Missing chrom sizes file, attempting to fetch for '%s'" % genome_build
81 # Run fetchChromSizes 85 # Run fetchChromSizes
82 chrom_sizes = os.path.join(working_dir,chrom_sizes) 86 chrom_sizes = os.path.join(working_dir,chrom_sizes)
83 stderr_file = os.path.join(working_dir,"fetchChromSizes.stderr") 87 stderr_file = os.path.join(working_dir,"fetchChromSizes.stderr")
84 cmd = "fetchChromSizes %s" % genome_build 88 cmd = "fetchChromSizes %s" % genome_build