--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_methylation_extractor.py	Sat Jul 06 09:57:36 2013 -0400
@@ -0,0 +1,191 @@
+#!/usr/bin/env python
+
+import argparse, os, shutil, subprocess, sys, tempfile, fileinput
+import zipfile
+from glob import glob
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def zipper(dir, zip_file):
+    zip = zipfile.ZipFile(zip_file, 'w', compression=zipfile.ZIP_DEFLATED)
+    root_len = len(os.path.abspath(dir))
+    for root, dirs, files in os.walk(dir):
+        archive_root = os.path.abspath(root)[root_len:]
+        for f in files:
+            fullpath = os.path.join(root, f)
+            archive_name = os.path.join(archive_root, f)
+            zip.write(fullpath, archive_name, zipfile.ZIP_DEFLATED)
+    zip.close()
+    return zip_file
+
+def __main__():
+    #Parse Command Line
+    parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.')
+
+    # input options
+    parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' )
+
+    parser.add_argument( '--infile', help='Input file in SAM format.' )
+    parser.add_argument( '--single-end', dest='single_end', action="store_true" )
+    parser.add_argument( '--paired-end', dest='paired_end', action="store_true" )
+
+    parser.add_argument( '--report-file', dest='report_file' )
+    parser.add_argument( '--comprehensive', action="store_true" )
+    parser.add_argument( '--merge-non-cpg', dest='merge_non_cpg', action="store_true" )
+    parser.add_argument( '--no-overlap', dest='no_overlap', action="store_true" )
+    parser.add_argument( '--compress' )
+    parser.add_argument( '--ignore-bps', dest='ignore_bps', type=int )
+
+    # OT - original top strand
+    parser.add_argument( '--cpg_ot' )
+    parser.add_argument( '--chg_ot' )
+    parser.add_argument( '--chh_ot' )
+    # CTOT - complementary to original top strand
+    parser.add_argument( '--cpg_ctot' )
+    parser.add_argument( '--chg_ctot' )
+    parser.add_argument( '--chh_ctot' )
+    # OB - original bottom strand
+    parser.add_argument( '--cpg_ob' )
+    parser.add_argument( '--chg_ob' )
+    parser.add_argument( '--chh_ob' )
+    # CTOT - complementary to original bottom strand
+    parser.add_argument( '--cpg_ctob' )
+    parser.add_argument( '--chg_ctob' )
+    parser.add_argument( '--chh_ctob' )
+
+    parser.add_argument( '--cpg_context' )
+    parser.add_argument( '--chg_context' )
+    parser.add_argument( '--chh_context' )
+
+    parser.add_argument( '--non_cpg_context' )
+
+    parser.add_argument( '--non_cpg_context_ot' )
+    parser.add_argument( '--non_cpg_context_ctot' )
+    parser.add_argument( '--non_cpg_context_ob' )
+    parser.add_argument( '--non_cpg_context_ctob' )
+
+    args = parser.parse_args()
+
+
+    # Build methylation extractor command
+    output_dir = tempfile.mkdtemp()
+    cmd = 'bismark_methylation_extractor --no_header -o %s %s %s'
+    if args.bismark_path:
+        # add the path to the bismark perl scripts, that is needed for galaxy
+        cmd = os.path.join(args.bismark_path, cmd)
+
+    additional_opts = ''
+    # Set up all options
+    if args.single_end:
+        additional_opts += ' --single-end '
+    else:
+        additional_opts += ' --paired-end '
+    if args.no_overlap:
+        additional_opts += ' --no_overlap '
+    if args.ignore_bps:
+        additional_opts += ' --ignore %s ' % args.ignore_bps
+    if args.comprehensive:
+        additional_opts += ' --comprehensive '
+    if args.merge_non_cpg:
+        additional_opts += ' --merge_non_CpG '
+    if args.report_file:
+        additional_opts += ' --report '
+
+
+    # Final command:
+    cmd = cmd % (output_dir, additional_opts, args.infile)
+
+    # Run
+    try:
+        tmp_out = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp_out, 'wb' )
+        tmp_err = tempfile.NamedTemporaryFile().name
+        tmp_stderr = open( tmp_err, 'wb' )
+        proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        # get stderr, allowing for case where it's very large
+        tmp_stderr = open( tmp_err, 'rb' )
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stdout.close()
+        tmp_stderr.close()
+        if returncode != 0:
+            raise Exception, stderr
+            
+        # TODO: look for errors in program output.
+    except Exception, e:
+        stop_err( 'Error in bismark methylation extractor:\n' + str( e ) ) 
+
+
+    # collect and copy output files
+
+    if args.compress:
+        zipper(output_dir, args.compress)
+
+
+    if args.cpg_ot:
+        shutil.move( glob(os.path.join( output_dir, '*CpG_OT_*'))[0], args.cpg_ot )
+    if args.chg_ot:
+        shutil.move( glob(os.path.join( output_dir, '*CHG_OT_*'))[0], args.chg_ot )
+    if args.chh_ot:
+        shutil.move( glob(os.path.join( output_dir, '*CHH_OT_*'))[0], args.chh_ot )
+    if args.cpg_ctot:
+        shutil.move( glob(os.path.join( output_dir, '*CpG_CTOT_*'))[0], args.cpg_ctot )
+    if args.chg_ctot:
+        shutil.move( glob(os.path.join( output_dir, '*CHG_CTOT_*'))[0], args.chg_ctot )
+    if args.chh_ctot:
+        shutil.move( glob(os.path.join( output_dir, '*CHH_CTOT_*'))[0], args.chh_ctot )
+    if args.cpg_ob:
+        shutil.move( glob(os.path.join( output_dir, '*CpG_OB_*'))[0], args.cpg_ob )
+    if args.chg_ob:
+        shutil.move( glob(os.path.join( output_dir, '*CHG_OB_*'))[0], args.chg_ob )
+    if args.chh_ob:
+        shutil.move( glob(os.path.join( output_dir, '*CHH_OB_*'))[0], args.chh_ob )
+    if args.cpg_ctob:
+        shutil.move( glob(os.path.join( output_dir, '*CpG_CTOB_*'))[0], args.cpg_ctob )
+    if args.chg_ctob:
+        shutil.move( glob(os.path.join( output_dir, '*CHG_CTOB_*'))[0], args.chg_ctob )
+    if args.chh_ctob:
+        shutil.move( glob(os.path.join( output_dir, '*CHH_CTOB_*'))[0], args.chh_ctob )
+
+    # context-dependent methylation output files
+    if args.cpg_context:
+        shutil.move( glob(os.path.join( output_dir, '*CpG_context_*'))[0], args.cpg_context )
+    if args.chg_context:
+        shutil.move( glob(os.path.join( output_dir, '*CHG_context_*'))[0], args.chg_context )
+    if args.chh_context:
+        shutil.move( glob(os.path.join( output_dir, '*CHH_context_*'))[0], args.chh_context )
+
+    if args.non_cpg_context:
+        shutil.move( glob(os.path.join( output_dir, '*Non_CpG_context_*'))[0], args.non_cpg_context )
+
+    if args.non_cpg_context_ot:
+        shutil.move( glob(os.path.join( output_dir, '*Non_CpG_OT_*'))[0], args.non_cpg_context_ot )
+    if args.non_cpg_context_ctot:
+        shutil.move( glob(os.path.join( output_dir, '*Non_CpG_CTOT_*'))[0], args.non_cpg_context_ctot )
+    if args.non_cpg_context_ob:
+        shutil.move( glob(os.path.join( output_dir, '*Non_CpG_OB_*'))[0], args.non_cpg_context_ob )
+    if args.non_cpg_context_ctob:
+        shutil.move( glob(os.path.join( output_dir, '*Non_CpG_CTOB_*'))[0], args.non_cpg_context_ctob )
+
+
+
+    if args.report_file:
+        shutil.move( glob(os.path.join( output_dir, '*_splitting_report*'))[0], args.report_file )
+
+
+    # Clean up temp dirs
+    if os.path.exists( output_dir ):
+        shutil.rmtree( output_dir )
+
+if __name__=="__main__": __main__()