--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hint_wrapper.py	Wed May 24 00:35:42 2017 -0400
@@ -0,0 +1,72 @@
+#!/usr/bin/python
+
+import optparse, os, shutil, sys, tempfile, glob, shlex, vcf, pysam, tarfile
+from subprocess import *
+import subprocess
+
+CHUNK_SIZE = 2**20 #1mb
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def __main__():
+    parser = optparse.OptionParser()
+    parser.add_option('','--input', dest="inputF", action='store', type="string", default=None, help='')
+    parser.add_option('','--region', dest="regionF", action='store', type="string", default=None, help='')
+    parser.add_option( '', '--output', dest='outputF', action='store', type="string", default=None, help='')
+    parser.add_option( '', '--out-dir', dest='output_dir', action='store', type="string", default=None, help='If specified, the output directory for extra files.' )
+
+    (options, args) = parser.parse_args()
+
+    if not os.path.exists(options.output_dir): 
+        os.mkdir(options.output_dir)
+    input_dir = "%s/input" % options.output_dir
+    output_dir = "%s/output" % options.output_dir
+    config_dir = "%s/config" % options.output_dir
+           
+    if not os.path.exists(output_dir):
+        os.mkdir(input_dir)
+        os.mkdir(output_dir)
+        os.mkdir(config_dir)
+    # region input file
+    linked_bed_name = "%s/regions.bed" % input_dir
+    os.symlink(options.regionF, linked_bed_name)
+    linked_bam_name="%s/sample.bam" % input_dir
+    os.symlink(options.inputF, linked_bam_name)
+    pysam.index(linked_bam_name)
+    
+    input_config = open("%s/input.txt" % config_dir, 'w')
+    input_config.write("name\ttype\tfile\tdata\tgroup\n")
+    input_config.write("HS2\tregions\t%s\tHS\tDU_K562_HINT\n" % linked_bed_name) 
+    input_config.write("DNase\treads\t%s\tDNASE\tDU_K562_HINT\n" % linked_bam_name)
+    input_config.close()
+
+    hint_cmd = "rgt-hint --output-location %s/ %s/input.txt"  % (output_dir, config_dir)
+    print "hint cmd:%s" % hint_cmd
+    stdout = tempfile.NamedTemporaryFile( prefix="hint-stdout-", dir=options.output_dir)
+    stderr = tempfile.NamedTemporaryFile( prefix="hint-stderr-", dir=options.output_dir)
+    proc = subprocess.Popen( args=hint_cmd, stdout=stdout, stderr=stderr, shell=True, cwd=options.output_dir )
+    return_code = proc.wait()
+
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+        stderr.flush()
+        stderr.seek(0)
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    stdout.close()
+                                                                                    
+    # copy files to final output locations
+    shutil.copy('%s/DU_K562_HINT.bed' % output_dir, options.outputF)
+    cleanup_before_exit( options.output_dir )
+
+if __name__=="__main__": __main__()
+