Mercurial > repos > yhoogstrate > samtools_parallel_mpileup

annotate test-data/generate_reads.py @ 0:460f0749aac5 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
author yhoogstrate
date Thu, 05 Nov 2015 07:49:02 -0500
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460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
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1 #!/usr/bin/env python
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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4 import random
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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5 import math
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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8 __version_info__ = ('1', '0', '0')
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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9 __version__ = '.'.join(__version_info__)
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12 class Region:
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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13 def __init__(self,start,stop,sequence):
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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14 self.start = start
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15 self.stop = stop
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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16 self.sequence = sequence.strip().replace("\n","").replace(" ","")
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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17 if(len(self.sequence) != self.getSpanningLength()):
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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18 print "ERROR: sequence length: "+str(len(self.sequence))+", while spanning region is: "+str(self.getSpanningLength())
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19 import sys
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20 sys.exit()
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22 def getSpanningLength(self):
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23 return abs(self.stop-self.start+1)
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25 class ReadSynthesizer:
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26 def __init__(self,chromosome):
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27 self.regions = []
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28 self.chromosome = chromosome
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30 def addRegion(self,region):
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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31 self.regions.append(region)
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32
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33 def produceReads(self,readDensity = 1,read_length = 50):
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34 """
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35 Produces uniform reads by walking iteratively over self.regions
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36 """
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37
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38 mRNA = self.getTotalmRNA()
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
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39 spanning_length = self.getRegionSpanningLength()
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40 n = spanning_length['total'] - read_length + 1
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41
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42 j = 0
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43 k = 0
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44
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45 for i in range(n):
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46 # "alpha is playing the role of k and beta is playing the role of theta"
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47 dd = max(0,int(round(random.lognormvariate(math.log(readDensity),0.5))))# Notice this is NOT a binomial distribution!!
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48
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49 for d in range(dd):
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50 sequence = mRNA[i:i+read_length]
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51
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52 if(random.randint(0,1) == 0):
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53 strand = 0
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54 else:
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55 strand = 16
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56 flag = strand + 0
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57
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58 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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59
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60 spanning_length['iter'][j] -= 1
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61 if(k >= self.regions[j].getSpanningLength()-1):
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62 j += 1
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63 k = 0
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64 else:
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65 k += 1
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66
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67 def getMappingString(self,length,j,offset):
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68 m = 0
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69
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70 out = ""
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71
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72 for i in range(length):
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73 k = i + offset
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75 if(k >= self.regions[j].getSpanningLength()):
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76 j += 1
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77
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78 out += str(m)+"M"
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79 out += (str(self.regions[j].start - self.regions[j-1].stop-1))+"N"
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80 m = 1
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81
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82 offset = -k
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diff changeset
83 else:
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
84 m += 1
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
85
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
86 out += str(m) + "M"
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
87
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
88
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
89 return out
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
90
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
91 def getRegionSpanningLength(self):
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
92 length = {'total':0,'iter':[]}
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
93 for r in self.regions:
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
94 l = r.getSpanningLength()
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
95 length['iter'].append(l)
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
96 length['total'] += l
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
97 return length
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
98
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
99 def getTotalmRNA(self):
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
100 mRNA = ""
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
101 for r in self.regions:
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
102 mRNA += r.sequence
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
103 return mRNA
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
104
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
105
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
106
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
107 if __name__ == "__main__":
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
108 # Artificial SNP
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
109 rs = ReadSynthesizer('chr1')
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
110 rs.addRegion(Region( 0+1, 59+1,'aaataggtcccaaacgttacgca'+'G'+'tctatgcctgacaaagttgcgaccacttcctctgcc'))#c -> G
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
111 rs.addRegion(Region( 60+1,119+1,'ttgtgtgacacgccggagatagg'+'A'+'catcagcaagtacgttaagtacactgaacgaactgg'))#g -> A
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
112 rs.addRegion(Region(120+1,179+1,'aggtttctacatcgtgcgtgatggc'+'C'+'ctaggagaagtgggtgtatctgcacagcataagt'))#t -> C
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
113 rs.addRegion(Region(180+1,239+1,'tataagacggaagtaaagcgtcttc'+'G'+'ccgttcagcaccccacgctcatagtcaatgctgg'))#a -> G
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
114 #rs.addRegion(Region(240+1,299+1,'ttcagcatagtcaagcgccggtggcctccaaaaagacgcactgagtagcttagctacttt'))
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
115 #rs.addRegion(Region(300+1,359+1,'gctccgcttgcggaagcactaagaggagattgaatttccaaatcccccccgatacctgtg'))
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
116 #rs.addRegion(Region(360+1,419+1,'cggtcgctacgtaagtgcgaagttctgttagatacgctccccttagtatatgggcgttaa'))
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
117 #rs.addRegion(Region(420+1,479+1,'tcggaccgtcggtactcactgcattccaggtctcatatagttcgccctagaagcctggga'))
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
118 rs.addRegion(Region(480+1,539+1,'tgaacgttgaacta'+'GCC'+'ctgatgtaaaccccgcgtgccaattccaggcgtcatgggggca'))#tag -> gcc
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
119 #rs.addRegion(Region(540+1,599+1,'acccctcgcagcctccctcttgctgttggtgcctagtatttcatgatttcgagccgacat'))
460f0749aac5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
yhoogstrate
parents:
diff changeset
120 rs.produceReads(2,35)