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38
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1 #!/usr/bin/env python
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2
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3
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4 import random
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5 import math
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6
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7
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8 class Region:
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9 def __init__(self,start,stop,sequence):
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10 self.start = start
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11 self.stop = stop
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12 self.sequence = sequence.strip().replace("\n","").replace(" ","")
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13 if(len(self.sequence) != self.getSpanningLength()):
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14 print "ERROR: sequence length: "+str(len(self.sequence))+", while spanning region is: "+str(self.getSpanningLength())
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15 import sys
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16 sys.exit()
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17
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18 def getSpanningLength(self):
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19 return abs(self.stop-self.start+1)
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20
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21 class ReadSynthesizer:
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22 def __init__(self,chromosome):
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23 self.regions = []
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24 self.chromosome = chromosome
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25
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26 def addRegion(self,region):
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27 self.regions.append(region)
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28
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29 def produceReads(self,readDensity = 1,read_length = 50):
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30 """
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31 Produces uniform reads by walking iteratively over self.regions
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32 """
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33
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34 mRNA = self.getTotalmRNA()
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35 spanning_length = self.getRegionSpanningLength()
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36 n = spanning_length['total'] - read_length + 1
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37
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38 j = 0
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39 k = 0
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40
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41 for i in range(n):
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42 # "alpha is playing the role of k and beta is playing the role of theta"
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43 dd = max(0,int(round(random.lognormvariate(math.log(readDensity),0.5))))# Notice this is NOT a binomial distribution!!
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44
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45 for d in range(dd):
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46 sequence = mRNA[i:i+read_length]
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47
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48 if(random.randint(0,1) == 0):
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49 strand = 0
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50 else:
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51 strand = 16
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52 flag = strand + 0
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53
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54 print "read_"+str(j)+"."+str(i)+"."+str(d)+"\t"+str(flag)+"\t"+self.chromosome+"\t"+str(self.regions[j].start + k)+"\t60\t"+self.getMappingString(read_length,j,k)+"\t*\t0\t0\t"+str(sequence.upper())+"\t*"
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55
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56 spanning_length['iter'][j] -= 1
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57 if(k >= self.regions[j].getSpanningLength()-1):
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58 j += 1
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59 k = 0
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60 else:
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61 k += 1
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62
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63 def getMappingString(self,length,j,offset):
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64 m = 0
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65
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66 out = ""
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67
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68 for i in range(length):
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69 k = i + offset
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70
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71 if(k >= self.regions[j].getSpanningLength()):
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72 j += 1
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73
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74 out += str(m)+"M"
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75 out += (str(self.regions[j].start - self.regions[j-1].stop-1))+"N"
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76 m = 1
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77
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78 offset = -k
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79 else:
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80 m += 1
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81
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82 out += str(m) + "M"
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83
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84
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85 return out
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86
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87 def getRegionSpanningLength(self):
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88 length = {'total':0,'iter':[]}
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89 for r in self.regions:
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90 l = r.getSpanningLength()
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91 length['iter'].append(l)
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92 length['total'] += l
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93 return length
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94
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95 def getTotalmRNA(self):
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96 mRNA = ""
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97 for r in self.regions:
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98 mRNA += r.sequence
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99 return mRNA
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100
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101 #rs = ReadSynthesizer('chr6')
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102 #rs.addRegion(Region(100,149,'ccaggactggtttctgtaagaaacagcaggagctgtggcagcggcgaaag'))
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103 #rs.addRegion(Region(151,152,'at'))
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104 #rs.produceReads(3,50)
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105
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106
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107 rs = ReadSynthesizer('chr6')
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108 rs.addRegion(Region(154360546,154360969,'ccaggactggtttctgtaagaaacagcaggagctgtggcagcggcgaaaggaagcggctgaggcgcttggaacccgaaaagtctcggtgctcctggctacctcgcacagcggtgcccgcccggccgtcagtaccatggacagcagcgctgcccccacgaacgccagcaattgcactgatgccttggcgtactcaagttgctccccagcacccagccccggttcctgggtcaacttgtcccacttagatggcGacctgtccgacccatgcggtccgaaccgcaccgacctgggcgggagagacagcctgtgccctccgaccggcagtccctccatgatcacggccatcacgatcatggccctctactccatcgtgtgcgtggtggggctcttcggaaacttcctggtcatgtatgtgattgtcag'))
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109 rs.addRegion(Region(154410961,154411313,'atacaccaagatgaagactgccaccaacatctacattttcaaccttgctctggcagatgccttagccaccagtaccctgcccttccagagtgtgaattacctaatgggaacatggccatttggaaccatcctttgcaagatagtgatctccatagattactataacatgttcaccagcatattcaccctctgcaccatgagtgttgatcgatacattgcagtctgccaccctgtcaaggccttagatttccgtactccccgaaatgccaaaattatcaatgtctgcaactggatcctctcttcagccattggtcttcctgtaatgttcatggctacaacaaaatacaggcaag'))
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110 rs.addRegion(Region(154412087,154412607,'gttccatagattgtacactaacattctctcatccaacctggtactgggaaaacctgctgaagatctgtgttttcatcttcgccttcattatgccagtgctcatcattaccgtgtgctatggactgatgatcttgcgcctcaagagtgtccgcatgctctctggctccaaagaaaaggacaggaatcttcgaaggatcaccaggatggtgctggtggtggtggctgtgttcatcgtctgctggactcccattcacatttacgtcatcattaaagccttggttacaatcccagaaactacgttccagactgtttcttggcacttctgcattgctctaggttacacaaacagctgcctcaacccagtcctttatgcatttctggatgaaaacttcaaacgatgcttcagagagttctgtatcccaacctcttccaacattgagcaacaaaactccactcgaattcgtcagaacactagagaccacccctccacggccaatacagtggatagaactaatcatcag'))
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111 rs.addRegion(Region(154428600,154428787,'gtggaattgaacctggactgtcactgtgaaaatgcaaagccttggccactgagctacaatgcagggcagtctccatttcccttcccaggaagagtctagagcattaattttgagtttgcaaaggcttgtaactatttcatatgatttttagagctgactatgacatgaaccctaaaattcctgttccc'))
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112 rs.produceReads(3,50)
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113
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115
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