diff utils.py @ 50:3e5b6f6a9abe draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty

--- a/utils.py	Wed Mar 29 14:46:23 2017 -0400
+++ b/utils.py	Thu Mar 30 16:03:16 2017 -0400
@@ -35,13 +35,11 @@
     except IOError as err:
         print "Cannot create tempfile err({0}): {1}".format(err.errno, err.strerror)
     try:
-        p = subprocess.Popen(['faToTwoBit', reference, twoBitFile.name])
-        p.communicate()
+        subprocess.call(['faToTwoBit', reference, twoBitFile.name])
     except OSError as err:
         print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
     try:
-        p = subprocess.Popen(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
-        p.communicate()
+        subprocess.call(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
     except OSError as err:
         print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
     return chrom_sizes
@@ -155,8 +153,7 @@
     return "gonramp_" + sanitized_name
 
 def createBamIndex(bamfile):
-    p = subprocess.Popen(['samtools', 'index', bamfile])
-    p.communicate()
+    subprocess.call(['samtools', 'index', bamfile])
     filename = bamfile + '.bai'
     if os.path.exists(filename):
         return filename