diff mdust_wrapper.py @ 2:79feb4eb7832 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mdust_wrapper.py	Wed Nov 18 10:51:42 2015 -0500
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+
+import subprocess
+import tempfile
+import sys
+import os
+import re
+from optparse import OptionParser
+
+
+class MdustWrapper(object):
+
+    def __init__(self):
+        self._options = None
+
+    def stop_err(self, msg):
+        sys.stderr.write("%s\n" % msg)
+        sys.exit()
+
+    def setAttributesFromCmdLine(self):
+        description = "mdust_wrapper"
+        description += "\nWrapper for mdust\n"
+        description += "example: mdust_wrapper.py -i seq.fasta -v 27\n"
+        parser = OptionParser(description = description, version = "0.1")
+        parser.add_option("-i", "--input",	   dest = "FastaFile",   action = "store", type = "string", help = "Input Fasta File name [compulsory] [format: Fasta]", default = "")
+        parser.add_option("-o", "--output",	dest = "outFile",   action = "store", type = "string", help = "output File name [compulsory] [format: fasta,tab or bed]", default = "")
+        parser.add_option("-v", "--cutoff",	 dest = "cutoff",	 action = "store", type = "int",	help = "cutoff",	default = 28)
+        parser.add_option("-w", "--wsize",	 dest = "wsize",	 action = "store", type = "int",	help = "window size",	default = 3)
+        parser.add_option("-m", "--maskingletter",	 dest = "maskingletter",	 action = "store", type = "string",	help = "masking letter",	default = "N")
+        parser.add_option("-f", "--format",	   dest = "format",  action = "store", type = "string", help = "format", default = "default")
+        options = parser.parse_args()[0]
+        self._setAttributesFromOptions(options)
+
+
+    def _setAttributesFromOptions(self, options):
+        self._options = options
+
+        if self._options.FastaFile == "":
+            raise Exception("Missing input file, please provide fasta file with -i file !")
+        if self._options.outFile == "":
+            raise Exception("Missing output file, please provide output file with -o file !")
+
+
+    def run(self):
+
+		prg = "mdust"
+		args = ""
+		args += " %s" % self._options.FastaFile
+                args += " -v %d" % self._options.cutoff
+                args += " -w %d" % self._options.wsize
+                args += " -m %s" % self._options.maskingletter
+                if self._options.format == "tab" or self._options.format == "bed":
+                    args += " -c "
+		cmd = "%s %s" %(prg, args)
+
+		try:
+			tmp_err = tempfile.NamedTemporaryFile().name
+                        tmp_out = "outfile"
+			tmp_stderr = open( tmp_err, 'wb' )
+			tmp_stdout = open( tmp_out, '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' )
+			tmp_stdout = open( tmp_out, 'rb' )
+
+			stderr = ''
+                        stdout = ''
+			buffsize = 1048576
+			try:
+				while True:
+					stdout += tmp_stdout.read( buffsize )
+					if not stdout or len( stdout ) % buffsize != 0:
+						break
+			except OverflowError:
+				pass
+			tmp_stdout.close()
+
+                        try:
+				while True:
+					stderr += tmp_stderr.read( buffsize )
+					if not stderr or len( stderr ) % buffsize != 0:
+						break
+			except OverflowError:
+				pass
+			tmp_stderr.close()
+			if stderr:
+				raise Exception, stderr
+		except Exception, e:
+			self.stop_err( 'Error with mdust :\n' + str( e ) )
+
+                if self._options.format == 'bed':
+                    with open(tmp_out,"r") as fin:
+                        with open(self._options.outFile, "w") as fout:
+                            lineNumber = 0
+                            for line in fin:
+                                lineNumber += 1
+                                m = re.search(r"^(\S+)\t(\d+)\t(\d+)\t(\d+)$", line)
+                                if m is not None:
+                                    fout.write("%s\t%d\t%d\n" % (m.group(1), int(m.group(3))-1, int(m.group(4))))
+                                if m is None:
+                                    raise Exception("\nLine %d '%s' does not has a mdust format." % (lineNumber, line))
+                else:
+                    os.rename(tmp_out,self._options.outFile)
+
+
+
+
+if __name__ == "__main__":
+	iWrapper = MdustWrapper()
+	iWrapper.setAttributesFromCmdLine()
+	iWrapper.run()