nonltr.py

mgescan/cmd.py

@@ -41,7 +41,7 @@ def __init__(self, args):
         self.set_inputs()
         self.set_defaults()
         self.get_env()
-        self.set_env()
+        self.set_debug()
 
     def set_inputs(self):
         self.data_dir = utils.get_abspath(self.args['--output'])
@@ -83,6 +83,10 @@ def set_defaults(self):
         self.scaffold = "" # or directory
 
     def get_env(self):
+        if not os.environ.get('MGESCAN_SRC'):
+            print ("MGEScan environment variable is not defined or .mgescanrc is not sourced.")
+            sys.exit(-1)
+        self.base_path = os.environ.get('MGESCAN_SRC') + "/mgescan"
         self.hmmerv = os.environ.get("MGESCAN_HMMER_VERSION") or self.hmmerv
         self.min_dist = os.environ.get("MGESCAN_MIN_DISTANCE") or self.min_dist
         self.max_dist = os.environ.get("MGESCAN_MAX_DISTANCE") or self.max_dist
@@ -93,15 +97,11 @@ def get_env(self):
         self.len_condition = os.environ.get("MGESCAN_MIN_LENGTH") or self.len_condition
         self.sw_rm = os.environ.get("MGESCAN_REPEATMASKER") or self.sw_rm
         self.scaffold = os.environ.get("MGESCAN_SCAFFOLD_DIR") or self.scaffold
-
-    def set_env(self):
-        self.base_path = os.environ.get('MGESCAN_SRC') + "/mgescan"
-        if not self.base_path:
-            print ("MGEScan environment (.mgescanrc) is not defined")
-            sys.exit(-1)
+
+    def set_debug(self):
         if self.debug:
             os.environ["MGESCAN_DEBUG"] = "True"
-            
+
     def wrapper_split_files(self):
         split = Split()
         split.set_input(self.genome_dir)

mgescan/nonltr/nonltr.py

@@ -1,24 +1,109 @@
+import os.path
+from mgescan import utils
 from docopt import docopt
-
+from multiprocessing import Process
 
 class NonLTR(object):
     """MGEScan Non-LTR
-    
+
     Usage:
-      nonltr.py <input> [--output=<output>]
+      nonltr.py <input> <output> [--mpi=<num>]
       nonltr.py -h | --help
       nonltr.py --version
 
     Options:
       -h --help     show help message
       --version     show version
-      --output=<output>     output directory to store results
 
     """
 
+    name = "nonltr"
+    ver = 'MGEScan NonLTR 3.0.0'
+    mpi_cmd = "mpi_mgescan"
+    hmmerv = "3"
+    tag_for_backward = "_b"
+
+    def __init__(self):
+        self.set_inputs()
+        self.get_env()
+        self.set_param()
+
+    def get_env(self):
+        self.base_path = os.environ.get("MGESCAN_SRC") + "/mgescan/"
+        self.hmmerv = os.environ.get("MGESCAN_HMMER_VERSION") or self.hmmerv
+
+    def set_param(self):
+        if self.nmpi:
+            self.p_np = "-n " + self.nmpi
+        self.p_prg = "--prg " + self.name
+        self.p_mgescan_mpi_cmd = self.base_path + self.mpi_cmd
+        self.p_genome_f = "--genome " + self.genome_path
+        self.p_genome_b = "--genome " + self.genome_path + self.tag_for_backward
+        self.p_data = "--data " + self.output_path
+        self.p_hmmerv = "--hmmerv " + self.hmmerv
+        self.set_mpi_option()
+
+    def set_mpi_option(self):
+        self.read_mpi_host_file()
+        self.p_mpi_option = self.p_hf_option + " -mca btl ^openib"
+
+    def read_mpi_host_file(self):
+        fname = os.environ.get("MGESCAN_SRC") + "host_file"
+        if os.path.isfile(fname):
+            self.p_hf_option = "-hostfile " + fname
+        self.p_hf_option = ""
+
+    def forward(self):
+        if self.nmpi:
+            cmd = self._padding("mpirun", self.p_np, self.p_mpi_option,
+                    self.p_mgescan_mpi_cmd, self.p_prg, self.p_genome_f,
+                    self.p_data, self.p_hmmerv)
+            self.run_cmd(cmd)
+
+    def backward(self):
+        if self.nmpi:
+            cmd = self._padding("mpirun", self.p_np, self.p_mpi_option,
+                    self.p_mgescan_mpi_cmd, self.p_prg, self.p_genome_b,
+                    self.p_data, self.p_hmmerv)
+            self.run_cmd(cmd)
+
+    def _padding(self, *args):
+        res = ""
+        for i in args:
+            res = res + " " + i
+        if len(res) > 1:
+            return res[1:]
+        else:
+            return res
+    def run_cmd(self, cmd):
+        print cmd
+        return
+        try:
+            retcode = check_call(cmd.split())
+            if retcode < 0:
+                print >>sys.stderr, "%s was terminated by signal" % cmd, -retcode
+            else:
+                print >>sys.stderr, "Returned", retcode
+        except OSError as e:
+            print >>sys.stderr, "Failed:", e
+        return retcode
+
+    def set_inputs(self):
+        self.args = docopt(self.__doc__, version=self.ver)
+        self.nmpi = self.args['--mpi']
+        self.genome_path = utils.get_abspath(self.args['<input>'])
+        self.output_path = utils.get_abspath(self.args['<output>'])
+
     def run(self):
-        arguments = docopt(self.__doc__, version='MGEScan NonLTR 2.0')
-        print arguments
+        p1 = Process(target=self.forward)
+        p2 = Process(target=self.backward)
+        p1.start()
+        p2.start()
+
+        if 'p1' in locals():
+            p1.join()
+        if 'p2' in locals():
+            p2.join()
 
 if __name__ == '__main__':
     obj = NonLTR()