--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/galaxy/bs_seeker2_wrapper.py	Fri Jul 12 18:47:28 2013 -0400
@@ -0,0 +1,123 @@
+import tempfile
+
+__author__ = 'pf'
+from subprocess import Popen
+from collections import defaultdict
+import sys, shutil, os, re
+
+
+
+BUILD = 'build'
+ALIGN = 'align'
+CALL_METHYLATION = 'call_methylation'
+
+EXEC = 'exec'
+EXEC_PATH = EXEC+'-path'
+ARG_TYPES = [BUILD, ALIGN, CALL_METHYLATION, EXEC]
+
+USAGE = """
+%(script)s is a wrapper script for bs_seeker2-build.py and bs_seeker2-align.py that is intended to be used with the Galaxy web platform.
+The script takes command line parameters and runs bs_seeker2-align.py and bs_seeker2-build.py, if neccessary.
+
+The parameters that are related to bs_seeker2-build.py must be prefixed with --%(build_tag)s.
+The parameters that are related to bs_seeker2-align.py must be prefixed with --%(align_tag)s.
+Additionally, the path to BS-Seeker2 has to be specified via the --%(exec_path)s option.
+
+For example:
+
+    python %(script)s --%(exec_path)s /mnt/Data/UCLA/Matteo/BS-Seeker --build-f data/arabidopsis/genome/Arabidopsis.fa --align-i data/arabidopsis/BS6_N1try2L7_seq.txt.fa --align-o data/arabidopsis/BS6_N1try2L7_seq.txt.fa.test_output
+
+This will run build the genome in Arabidopsis.fa and put the indexes in a temporary directory. bs_seeker2-align.py will be run on the
+newly created genome index. I.e. the following two commands will be run in a shell:
+
+    python /mnt/Data/UCLA/Matteo/BS-Seeker/bs_seeker2-build.py --db /tmp/tmpg8Eq1o -f /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/genome/Arabidopsis.fa
+
+    python /mnt/Data/UCLA/Matteo/BS-Seeker/bs_seeker2-align.py --db /tmp/tmpg8Eq1o -o /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/BS6_N1try2L7_seq.txt.fa.test_output -i /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/BS6_N1try2L7_seq.txt.fa -g Arabidopsis.fa
+
+
+The temporary directory will be deleted after the wrapper exits.
+
+
+If no options related to bs_seeker2-build are passed, no genome index will be built and the corresponding pre-built genome index will be used
+instead. No temporary files and directories will be created.
+
+""" % { 'script' : os.path.split(__file__)[1], 'build_tag' :BUILD, 'align_tag' : ALIGN, 'exec_path' : EXEC_PATH }
+
+
+def error(msg):
+    print >> sys.stderr, 'ERROR: %s' % msg
+    exit(1)
+
+
+if __name__ == '__main__':
+    if len(sys.argv) == 1:
+        error('No parameters\n\n'+USAGE)
+
+
+    # Parse command line arguments
+    args = defaultdict(dict)
+    arg_key = None
+    arg_val = None
+    arg_type = None
+
+    for arg in sys.argv[1:]:
+        if arg.startswith('--'):
+            try:
+                arg_type, arg_key = re.match(r'--(\w+)(.*)', arg).groups()
+                if arg_type not in ARG_TYPES:
+                    raise Exception("Bad argument: %s. arg_type (%s) must be one of: %s." % (arg, arg_type, ', '.join(ARG_TYPES)))
+                if not arg_key or arg_key[0] != '-':
+                    raise Exception("Bad argument: %s. arg_key (%s) must start with - or --." % (arg, arg_key))
+            except Exception, e:
+                error(str(e) + '\n\n' + USAGE)
+            args[arg_type][arg_key] = ''
+        else:
+            args[arg_type][arg_key] = arg
+
+    path_to_bs_seeker = args.get('exec', {'-path' : None})['-path'] # return None when exec not found
+    if path_to_bs_seeker is None:
+        error('You have to specify the path to BS-Seeker2 via --%s\n\n' % EXEC_PATH + USAGE)
+
+    tempdir = None
+    def run_prog(prog, params):
+        cwd, _ = os.path.split(__file__)
+        cmd = 'python %(prog)s %(params)s' % {
+                   'prog'   : os.path.join(cwd, prog),
+                   'params' : ' '.join('%s %s' % (arg_key, arg_val) for arg_key, arg_val in params.items())
+                   }
+        print 'exec:', cmd
+
+        return_code = Popen(args = cmd, shell = True).wait()
+        if return_code:
+            if tempdir:
+                shutil.rmtree(tempdir)
+            error("%s exit with error code %d" % (prog, return_code))
+    tempdir = tempfile.mkdtemp()
+
+    # bs_seeker2-build
+    if BUILD in args:
+        args[BUILD]['--db'] = tempdir
+        args[ALIGN]['--db'] = tempdir
+        run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-build.py'), args[BUILD])
+
+    # bs_seeker2-align
+    args[ALIGN]['--temp_dir'] = tempdir
+    run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-align.py'), args[ALIGN])
+
+
+    def getopt(h, k1, k2, default):
+        return h.get(k1, h.get(k2, default))
+    # bs_seeker2-call_methylation
+    args[CALL_METHYLATION].update({  '-i'    : args[ALIGN]['--output'],
+                                     '--db'  : os.path.join(args[ALIGN]['--db'],
+                                    os.path.split(  getopt(args[ALIGN],'-g', '--genome', None))[1] +
+                                    ('_rrbs_%s_%s' % (getopt(args[ALIGN], '-l', '--low', '40'),
+                                                      getopt(args[ALIGN], '-u', '--up', '500'))
+                                     if len(set(['-r', '--rrbs']) & set(args[ALIGN])) > 0 else '') +
+
+                                    '_' + args[ALIGN]['--aligner'])
+                                    })
+    run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-call_methylation.py'), args[CALL_METHYLATION])
+
+    if tempdir:
+        shutil.rmtree(tempdir)
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