# HG changeset patch
# User bobbledavidson
# Date 1442397493 14400
# Node ID b970ba62539e3f6428c45e952ce2bc5f2cec6985
# Parent  9e8de4ce2a3cfede53a2def2d36fd59cf00dab12
Updated beagle4.py to output uncompressed VCF files - had been outputting VCF.GZ

diff -r 9e8de4ce2a3c -r b970ba62539e beagle4.py
--- a/beagle4.py	Wed Jul 08 11:08:07 2015 -0400
+++ b/beagle4.py	Wed Sep 16 05:58:13 2015 -0400
@@ -3,6 +3,7 @@
 import tempfile
 import shutil
 from subprocess import call
+import gzip 
 
 def main():
   
@@ -34,11 +35,16 @@
     	call(['java', '-Xmx2g', '-jar', options.jarfile, options.gtgl+'='+options.gfile,'phase-its='+options.phits, 'impute-its='+options.impits , 'out='+outdir+'/'+outprefix ])
    
 
-    shutil.move(outdir+'/'+outprefix+'.vcf.gz',options.outfile)
+    #shutil.move(outdir+'/'+outprefix+'.vcf.gz',options.outfile)
+    #shutil.rmtree(outdir)
+    with gzip.open(outdir+os.sep+outprefix+'.vcf.gz','rb') as gzinfile:
+        with open(options.outfile,'w') as vcfoutfile:
+            for line in gzinfile:
+                vcfoutfile.write(line)
+
     shutil.rmtree(outdir)
 
 
-
 if __name__=='__main__':
     main()