Mercurial > repos > pjbriggs > macs21

diff 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
line wrap: on
line diff
--- a/macs21_wrapper.py	Tue Apr 21 07:53:37 2015 -0400
+++ b/macs21_wrapper.py	Tue Apr 21 08:29:16 2015 -0400
@@ -77,6 +77,10 @@
         # Determine genome build
         chrom_sizes = os.path.basename(chrom_sizes)
         genome_build = chrom_sizes.split('.')[0]
+        if genome_build == '?':
+            # No genome build set
+            sys.stderr.write("ERROR genome build not set, cannot get sizes for '?'\n")
+            sys.exit(1)
         print "Missing chrom sizes file, attempting to fetch for '%s'" % genome_build
         # Run fetchChromSizes
         chrom_sizes = os.path.join(working_dir,chrom_sizes)