annotate test-data/create_test-data @ 0:6e75a84e9338 draft

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author thondeboer
date Tue, 15 May 2018 02:39:53 -0400 (2018-05-15)
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1 #!/bin/bash
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2 source ~/env/bin/activate
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4 samtools faidx chrMT.fa
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5 #TEST1: single read, with everything default
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6 python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1
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7 mv out_read1.fq chrMT_read1.fq
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8
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9 #TEST2: PE reads, with everything default
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10 python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30
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11 mv out_read1.fq chrMT-PE_read1.fq
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12 mv out_read2.fq chrMT-PE_read2.fq
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14 #TEST3: PE reads, with everything default, now with VCF and BAM files
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15 python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam
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16 mv out_read1.fq chrMT-PE-VCF-BAM_read1.fq
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17 mv out_read2.fq chrMT-PE-VCF-BAM_read2.fq
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18 mv out_golden.bam chrMT-PE-VCF-BAM.bam
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19 mv out_golden.vcf chrMT-PE-VCF-BAM.vcf
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21 samtools index chrMT-PE-VCF-BAM.bam
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23 #TEST4: PE reads, with VCF and BAM files and VCF file from TEST3 as the seed
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24 python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam -v chrMT-PE-VCF-BAM.vcf
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25 mv out_read1.fq chrMT-PE-VCF-BAM-vcf_read1.fq
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26 mv out_read2.fq chrMT-PE-VCF-BAM-vcf_read2.fq
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27 mv out_golden.bam chrMT-PE-VCF-BAM-vcf.bam
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28 mv out_golden.vcf chrMT-PE-VCF-BAM-vcf.vcf
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30 samtools index chrMT-PE-VCF-BAM-vcf.bam
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31
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32 #TEST5: PE reads, with VCF and BAM files and BED file as the targeted region
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33 python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam -t chrMT-Targets.bed -to 0.02
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34 mv out_read1.fq chrMT-PE-VCF-BAM-Targeted_read1.fq
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35 mv out_read2.fq chrMT-PE-VCF-BAM-Targeted_read2.fq
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36 mv out_golden.bam chrMT-PE-VCF-BAM-Targeted.bam
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37 mv out_golden.vcf chrMT-PE-VCF-BAM-Targeted.vcf
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39 samtools index chrMT-PE-VCF-BAM-Targeted.bam
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40
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41 #TEST6: PE reads, with everything default, now with VCF and BAM files GZIPPED
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42 python2 ../genReads.py -r chrMT.fa -R 101 -o out --rng 1 --pe 300 30 --vcf --bam --gz
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43 mv out_read1.fq.gz chrMT-PE-VCF-BAM-gz_read1.fq.gz
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44 mv out_read2.fq.gz chrMT-PE-VCF-BAM-gz_read2.fq.gz
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45 mv out_golden.bam chrMT-PE-VCF-BAM-gz.bam
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46 #Galaxy does not support gzipped VCF file (not sure if this is BGZIPPED)
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47 gunzip out_golden.vcf.gz && mv out_golden.vcf chrMT-PE-VCF-BAM-gz.vcf
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48
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49 samtools index chrMT-PE-VCF-BAM-gz.bam
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50
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51 #TEST7: PE reads, with all error parameters changed, with VCF and BAM files, not compressed
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52 python2 ../genReads.py -r chrMT.fa -R 151 -o out --rng 123 --pe 500 50 --vcf --bam -c 20 -E 0.123 -M 0.123 -p 3
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53 mv out_read1.fq chrMT-PE-VCF-BAM-panic_read1.fq
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54 mv out_read2.fq chrMT-PE-VCF-BAM-panic_read2.fq
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55 mv out_golden.bam chrMT-PE-VCF-BAM-panic.bam
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56 mv out_golden.vcf chrMT-PE-VCF-BAM-panic.vcf
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57
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58 samtools index chrMT-PE-VCF-BAM-panic.bam
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59
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60 #####
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61 # computeGC TESTS
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62 #
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63
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64 #TEST1: Use BAM from TEST3 to create the model file. Window size = 10
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65 bedtools genomecov -d -ibam chrMT-PE-VCF-BAM.bam -g chrMT.fa > chrMT-PE-VCF-BAM.genomecov
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66 python2 ../utilities/computeGC.py -r chrMT.fa -i chrMT-PE-VCF-BAM.genomecov -w 10 -o chrMT-PE-VCF-BAM-computeGC.p
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67
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68 #####
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69 # computeFraglen
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70 #
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71 samtools view chrMT-PE-VCF-BAM.bam | python2 ../utilities/computeFraglen.py
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72 mv fraglen.p chrMT-PE-VCF-BAM-fraglen.p
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73
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74 #####
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75 # genMutModel
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76 #
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77
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78 #TEST1: Default settings
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79 python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-genMutModel.p
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80
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81 #TEST2: Defined include list
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82 python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-INCLUDELIST-genMutModel.p\
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83 -bi chrMT-Targets.bed
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84
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85 #TEST3: Defined exclude list
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86 python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-EXCLUDELIST-genMutModel.p\
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87 -be chrMT-Targets.bed
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88
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89 #TEST1: Default settings with all booleans set to YES
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90 python2 ../utilities/genMutModel.py -r chrMT.fa -m chrMT-PE-VCF-BAM.vcf -o chrMT-PE-VCF-BAM-BOOLEANS-genMutModel.p\
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91 --save-trinuc --no-whitelist --skip-common
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92
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93 #####
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94 # genSeqErrorModel
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95 #
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96
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97 #TEST1 - 100,000 simulations - Single read
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98 python2 ../utilities/genSeqErrorModel.py -i chrMT_read1.fq -s 100000 -o chrMT_read1_genSeqErrorModel.p
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99
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100 #TEST2 - 100,000 simulations - Paired reads
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101 python2 ../utilities/genSeqErrorModel.py -i chrMT-PE_read1.fq -i2 chrMT-PE_read2.fq -s 100000 -o chrMT-PE_read1_genSeqErrorModel.p
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102
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103 #TEST3 - 100,000 simulations - Only 100 reads
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104 python2 ../utilities/genSeqErrorModel.py -i chrMT-PE_read1.fq -i2 chrMT-PE_read2.fq -s 100000 -o chrMT-PE-100reads_read1_genSeqErrorModel.p -n 100