1 files changed, 125 insertions, 0 deletions
diff --git a/benchmarks/CUDA/MUM/genreads.py b/benchmarks/CUDA/MUM/genreads.py
new file mode 100644
index 0000000..4302470
--- /dev/null
+++ b/benchmarks/CUDA/MUM/genreads.py
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+# encoding: utf-8
+"""
+untitled.py
+
+Created by Cole Trapnell on 2007-04-26.
+Copyright (c) 2007 __MyCompanyName__. All rights reserved.
+"""
+
+import sys
+import getopt
+import random
+
+
+help_message = """
+genreads outputs a multi-FASTA file containing a random sampling of 
+read-sized subsequences of the provided reference sequence.  
+
+Usage:
+	genreads [options] <reference file> <length of reads> <# of reads>	
+	
+Options:
+	-m < % mismatch>   --mismatches=  the % of bases in each read that
+	                                  don't match the reference
+	-s <integer value> --seed=        the seed for the random number 
+	                                  generator
+"""
+
+
+class Usage(Exception):
+	def __init__(self, msg):
+		self.msg = msg
+
+
+def main(argv=None):
+
+	if argv is None:
+		argv = sys.argv
+	try:
+		try:
+			opts, args = getopt.getopt(argv[1:], "hSd:m:s:v", ["help","distribution=", "mismatches=", "seed=", "sort"])
+		except getopt.error, msg:
+			raise Usage(msg)
+	
+		mismatch = 0.0
+	
+		seed_val = 0
+		sorted = False
+		# option processing
+		for option, value in opts:
+			if option == "-v":
+				verbose = True
+			if option in ("-h", "--help"):
+				raise Usage(help_message)
+			if option in ("-d", "--distribution"):
+				dist = value
+			if option in ("-m", "--mismatches"):
+				mismatch = float(value)
+			if option in ("-s", "--seed"):
+				seed_val = long(value)
+			if option in ("-S", "--sort"):
+				sorted = True
+			
+		random.seed(seed_val)
+		
+		if len(args) != 3:
+			raise Usage(help_message)
+	
+		fasta_input = args[0]
+		read_length = int(args[1])
+		num_reads = int(args[2])
+	
+		#fasta_input = "NC_003997.fna"
+		#read_length = 47
+		#num_reads = 10000
+		
+		f = open(fasta_input, "r")
+		lines = f.readlines()
+		
+		if lines[0].find(">") == -1:
+			raise Usage("File is not FASTA format")
+	
+	
+		seq = "".join([line.strip() for line in lines[1:]])
+		
+#		for line in lines[1:]:
+#			line = line.strip()
+#			if line.find(">") != -1:
+#				raise("Multi-FASTA format not supported")
+#			seq += line
+
+
+
+		#print seq
+		L = len(seq)
+	
+		#allowable = range(0, L - read_length)
+		
+		rid = 0
+		
+		base_mismatcher = {
+			"A" : "C",
+			"C"	: "G",
+			"G" : "T",
+			"T" : "A"
+		}
+
+		reads = []
+		
+		for i in range(0, num_reads):
+			start = random.randint(0, L - read_length)
+			#assert start <= L - read_length
+			end = start + read_length
+
+			rid +=1
+			print ">" + "rid" + str(rid)
+			print seq[start:end]
+			
+	except Usage, err:
+		print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+		return 2
+
+
+if __name__ == "__main__":
+	sys.exit(main())