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#!/usr/bin/env python
# Copyright (c) 2016, The Regents of the University of California.
import sys, os
import random
seqLength = (8000, 12000)
class collectionOFiles(object):
def __init__(self, baseName, divisions, totalSize):
self.baseName = baseName
self.divisions = divisions
self.totalSize = totalSize
self.fileHandles = {}
for i in range(0, divisions):
filename = self.baseName + "_%d" % i
fh = open(filename, "wb")
divisor = 2 ** i
self.fileHandles[filename]= (fh, self.totalSize/divisor, 0)
def writeRecord(self, name, description, sequence):
toRemove = []
for filename in self.fileHandles:
file, limit, count = self.fileHandles[filename]
file.write("%s %s\n%s\n" % (name, description, sequence))
count += 1
if count >= limit:
file.close()
toRemove.append(filename)
else:
self.fileHandles[filename] = (file, limit, count)
for fh in toRemove:
self.fileHandles.pop(fh)
def finished(self):
return len(self.fileHandles) == 0
def genSeq(min, max):
"""
Generates a sequence with min <= length <= max
"""
choices = ['A','T','C','G']
result = []
length = random.randrange(min, max)
for i in range(0, length):
result.append(random.choice(choices))
if i % 80 == 0:
result.append('\n')
return "".join(result)
def createFastaFiles(filename, size, divisions):
cof = collectionOFiles(filename, divisions, size)
counter = 0
description="cdna:Genscan chromosome:PPYG2:6_qbl_hap2_random:95622:98297:1"
while(not cof.finished()):
name = ">GENSCAN00%d" % counter
sequence = genSeq(seqLength[0], seqLength[1])
cof.writeRecord(name, description, sequence)
counter += 1
return
if __name__ == '__main__':
if len(sys.argv) != 4:
print "Usage: <filename> <size> <divisions>"
exit(1)
filename = sys.argv[1]
size = int(sys.argv[2])
divisions = int(sys.argv[3])
createFastaFiles(filename, size, divisions)
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