Exemplo n.º 1
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def mm9_17():
    dm.deriveNewDataset("mm9.17.Imprinted_DMR.alleleSpecific_differentiallyMethylatedRegions_manuallyCurated.region",
                        "mm9_alleleSpecificDMR",
                        [],
                        [],
                        None,
                        None,
                        True)
Exemplo n.º 2
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def mm9_12():    
    dm.deriveNewDataset("mm9.12.Enhancer_p300.ChIPseq_p300_binding_sites_Visel2009_noPromoter.region",
                        "mm9_enhancers_Visel_all",
                        ["mm9.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region"],
                        [],
                        "max",
                        None,
                        True)
Exemplo n.º 3
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def mm9_19():
    dm.deriveNewDataset("mm9.19.CancerGene_Promoter.Promoter_region_ensemblGenesMinus10000ToPlus2000AroundTSS_cancerGeneCensus.region",
                        "mm9_CancerGene_Promoters",
                        [],
                        [],
                        None,
                        None,
                        True)
Exemplo n.º 4
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def mm9_7():
    dm.deriveNewDataset("mm9.7.NonCGI_Promoter.Promoter_centered_nonOverlapping_with_BonaFide_CGI.region",
                        "mm9.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region",
                        ["mm9.5.BonaFide_CGI.cgiHunter_oe0.6_gc50_len700.region"],
                        [],
                        None,
                        None,
                        True)
Exemplo n.º 5
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def mm9_5():
    dm.deriveNewDataset("mm9.5.BonaFide_CGI.cgiHunter_oe0.6_gc50_len700.region",
                        "mm9_CGI_CGIHunter_GG",
                        [],
                        [],
                        None,
                        700,
                        True)
Exemplo n.º 6
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def mm9_4():
    dm.deriveNewDataset("mm9.4.CpG_Island.cgiHunter_oe0.6_gc50_len200.region",
                        "mm9_CGI_CGIHunter_GG",
                        [],
                        [],
                        None,
                        200,
                        True)
Exemplo n.º 7
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def mm9_20():
    dm.deriveNewDataset("mm9.20.CellStateGene_Promoter.Promoter_region_ensemblGenesMinus10000ToPlus2000AroundTSS_manuallyCurated.region",
                        "mm9_CandidatePromoters",
                        [],
                        [],
                        None,
                        None,
                        True)
Exemplo n.º 8
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def hg18_13():    
    dm.deriveNewDataset("hg18.13.Enhancer_H3K4me2.ChIPseq_H3K4me2_sites_Heintzman2009_noPromoter.region",
                        "hg18_enhancers_Heintzman2009",
                        ["hg18.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region"],
                        [],
                        None,
                        None,
                        True)
Exemplo n.º 9
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def hg18_12():    
    dm.deriveNewDataset("hg18_support.12.DNaseI_HS_site.hg18_tCell_DNaseI_hypersensitive_sites_Boyle2008",
                        "hg18_DNAseCD4Sites",
                        [],
                        [],
                        None,
                        None,
                        True)

    
    dm.regionDatasets.update(regionDatasets_DNaseI_Duke)
    dm.mergeDatasets("hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged",regionDatasets_DNaseI_Duke.keys())
    dm.deriveNewDataset("hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2",
                        "hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged",
                        [],
                        [],
                        "max",
                        None,
                        True,
                        True)
#

    dm.regionDatasets.update(regionDatasets_DNaseI_Washington)

    dm.mergeDatasets("hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged",
                     regionDatasets_DNaseI_Washington.keys())

    dm.deriveNewDataset("hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites",
                 "hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged",
                 [],
                 [],
                 "max",
                 None,
                 True,
                 True)
    dm.mergeDatasets("hg18_support.12.All_DNaseI_datasets_merged",
                     ["hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites",
                      "hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2",
                      "hg18_support.12.DNaseI_HS_site.hg18_tCell_DNaseI_hypersensitive_sites_Boyle2008"
                      ])
    
    dm.deriveNewDataset("hg18.12.Open_Chromatin.DNase_FAIRE_peaks_ENCODE_noPromoter.region",
                        "hg18_support.12.All_DNaseI_datasets_merged",
                        ["hg18.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region"],
                        [],
                        "max",
                        None,
                        True,
                        True)
    dm.deriveNewDataset("hg18.12.Open_Chromatin.DNase_FAIRE_peaks_ENCODE_noPromoter_downsampledTo500k.region",
                 "hg18.12.Open_Chromatin.DNase_FAIRE_peaks_ENCODE_noPromoter.region",
                 [],
                 [],
                 None,
                 None,
                 True,
                 True,
                 500000)
Exemplo n.º 10
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def mm9_13():
    dm.deriveNewDataset(
                        "mm9.13.Enhancer_H3K4me2.ChIPseq_H3K4me2_sitesWithin1kbTo100kbOfPromoter_Meissner2008_noPromoter.region",
                        "mm9_enhancers_meissner_all",
                        ["mm9.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region"],
                        [],
                        "max",
                        None,
                        True)
Exemplo n.º 11
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def mm9_22():
    dm.regionDatasets.update(regionDatasetsRepeatsMM9)
    dm.deriveNewDataset("mm9.22.Repeat_DNA.repeatMasker_annotation_DNA_repeats.region",
                        "mm9_Repeat_DNA",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True)
Exemplo n.º 12
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def mm9_11():
    dm.deriveNewDataset("mm9.11.Conserved_Region.UCSC_mostConserved_minLength100_noPromoter_noCGI_noExon_noUTR.region",
                        "mm9_mostConserved_all",
                 ["mm9.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region",
                  "mm9.4.CpG_Island.cgiHunter_oe0.6_gc50_len200.region",
                  "mm9_RefSeq_allCodingExons","mm9_RefSeq_3UTR"],
                  [],
                 "max",
                 100,
                 True)
Exemplo n.º 13
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def mm9_9(): 
    dm.deriveNewDataset("mm9.9.Middle_Exon.refSeqGenes_exon_noPromoter_noUTR.region",
                    "mm9_RefSeq_middleExons",
                    ["mm9.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region",
                     "mm9_RefSeq_3UTR"],
                     [],
                    "max",
                    None,
                    True,
                    True)
Exemplo n.º 14
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def hg18_22():
    dm.regionDatasets.update(regionDatasetsRepeatsHG18)
    dm.deriveNewDataset("hg18.22.Repeat_DNA.repeatMasker_annotation_DNA_repeats.region",
                        "hg18_Repeat_DNA",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True)
Exemplo n.º 15
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def hg18_24():
    dm.regionDatasets.update(regionDatasetsRepeatsHG18)
    dm.deriveNewDataset("hg18.24.Repeat_LowComplex.repeatMasker_annotation_low_complexity_repeats.region",
                        "hg18_Repeat_LowComplex",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True)
Exemplo n.º 16
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def hg18_26():
    dm.regionDatasets.update(regionDatasetsRepeatsHG18)
    dm.deriveNewDataset("hg18.26.Repeat_Simple.repeatMasker_annotation_simple_repeats.region",
                        "hg18_Repeat_Simple",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True)
Exemplo n.º 17
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def mm9_24():
    dm.regionDatasets.update(regionDatasetsRepeatsMM9)
    dm.deriveNewDataset("mm9.24.Repeat_LowComplex.repeatMasker_annotation_low_complexity_repeats.region",
                        "mm9_Repeat_LowComplex",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True)
Exemplo n.º 18
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def mm9_8():
    dm.extractFlanks("mm9_refseq_genes",
                     "mm9_support.8.refseq_genes_plus10k",
                     False,"whole_region",10000,10000)
    dm.deriveNewDataset("mm9.8.NonGenic_CGI.cgiHunter_oe0.6_gc50_len200_geneDistance10000.region",
                        "mm9.4.CpG_Island.cgiHunter_oe0.6_gc50_len200.region",
                        ["mm9_support.8.refseq_genes_plus10k"],
                        [],
                        None,
                        None,
                        True)
Exemplo n.º 19
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def mm9_10():
    dm.deriveNewDataset(
                "mm9.10.3prim_UTR.refSeqGenes_3prim_UTR_noPromoter_noExon.region",
                "mm9_RefSeq_3UTR",
                 ["mm9.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region",
                  "mm9_RefSeq_allCodingExons"],
                  [],
                 "max",
                 None,
                 True,
                 True)
Exemplo n.º 20
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def mm9_1():
    dm.extractFlanks("mm9_ensembl_genes",
                     "mm9_support.1.Promoter_ensembl.ensemblGenes_minus_5000_to_1000_around_TSS_flancks",
                     True,"start",5000,1000)
    dm.deriveNewDataset("mm9.1.Promoter_ensembl.ensemblGenes_minus_5000_to_1000_around_TSS.region",
                     "mm9_support.1.Promoter_ensembl.ensemblGenes_minus_5000_to_1000_around_TSS_flancks",
                     [],
                     [],
                     None,
                     None,
                     True,
                     True)
Exemplo n.º 21
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def hg18_3():
    dm.extractFlanks("hg18_refseq_genes",
                     "hg18_support.3.Promoter_region.refSeqGenes_minus_10000_to_2000_around_TSS_flancks",
                     True,"start",10000,2000)
    dm.deriveNewDataset("hg18.3.Promoter_region.refSeqGenes_minus_10000_to_2000_around_TSS.region",
                        "hg18_support.3.Promoter_region.refSeqGenes_minus_10000_to_2000_around_TSS_flancks",
                        [],
                        [],
                        "max",
                        None,
                        True,
                        True)
Exemplo n.º 22
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def hg18_2():
    dm.extractFlanks("hg18_refseq_genes",
                     "hg18_support.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS_flancks",
                     True,"start",1000,1000)
    dm.deriveNewDataset("hg18.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region",
                        "hg18_support.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS_flancks",
                        [],                        
                        [],
                        None,
                        None,
                        True,
                        True)
Exemplo n.º 23
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def hg18_6():
#    dm.deriveNewDataset("hg18.6.CGI_Promoter.Promoter_centered_overlapping_with_BonaFide_CGI.region",
#                        "hg18.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region",
#                        ["hg18.7.NonCGI_Promoter.Promoter_centered_nonOverlapping_with_BonaFide_CGI.region"],
#                        [],
#                        None,
#                        None,
#                        True)
    dm.deriveNewDataset("hg18.6.CGI_Promoter.Promoter_centered_overlapping_with_BonaFide_CGI.region",
                        "hg18.2.Promoter_centered.refSeqGenes_minus_1000_to_1000_around_TSS.region",
                        [],
                        ["hg18.5.BonaFide_CGI.cgiHunter_oe0.6_gc50_len700.region"],
                        None,
                        None,
                        True)
Exemplo n.º 24
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def CancerGenePromoterSufficientMethylationOverlappingWithCGI():
    cancerDataset = {
            "cancerPromoters_withMethylation":defaultFolder+"mm9.19.CancerGene_Promoter.Promoter_region_ensemblGenesMinus10000ToPlus2000AroundTSS_cancerGeneCensus.region_withMathylation.txt",
            }
    dm.regionDatasets.update(cancerDataset)
    mm9_4()
    
    dm.deriveNewDataset("mm9.cancerPRomoters_CGI",
                        "cancerPromoters_withMethylation",
                        [],                        
                        ["mm9.4.CpG_Island.cgiHunter_oe0.6_gc50_len200.region"],
                        None,
                        None,
                        True,
                        True)
Exemplo n.º 25
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def mm9_14():
    dm.extractFlanks("mm9.4.CpG_Island.cgiHunter_oe0.6_gc50_len200.region",
                     "mm9_support.14.CGI200_downstream",
                     False,"start",2000,0)
    dm.extractFlanks("mm9.4.CpG_Island.cgiHunter_oe0.6_gc50_len200.region",
                     "mm9_support.14.CGI200_upstream",
                     False,"end",0,2000)
    dm.mergeDatasets("mm9_support.14.CpG_Island_Shore.cgiHunter_oe0.6_gc50_len200_2kb_outsideCgi",
                     ["mm9_support.14.CGI200_upstream",
                      "mm9_support.14.CGI200_downstream"])
    dm.deriveNewDataset("mm9.14.CpG_Island_Shore.cgiHunter_oe0.6_gc50_len200_2kb_outsideCgi.region",
                        "mm9_support.14.CpG_Island_Shore.cgiHunter_oe0.6_gc50_len200_2kb_outsideCgi",
                        [],
                        [],
                        "max",
                        None,
                        True)    
Exemplo n.º 26
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def mm9_15():
    dm.extractFlanks("mm9.5.BonaFide_CGI.cgiHunter_oe0.6_gc50_len700.region",
                     "mm9_support.15.CGI700_downstream",
                     False,"start",2000,0)
    dm.extractFlanks("mm9.5.BonaFide_CGI.cgiHunter_oe0.6_gc50_len700.region",
                     "mm9_support.15.CGI700_upstream",
                     False,"end",0,2000)
    dm.mergeDatasets("mm9_support.15.BonaFide_CGI_Shore.cgiHunter_oe0.6_gc50_len700_2kb_outsideCgi",
                     ["mm9_support.15.CGI700_downstream",
                      "mm9_support.15.CGI700_upstream"])
    dm.deriveNewDataset("mm9.15.BonaFide_CGI_Shore.cgiHunter_oe0.6_gc50_len700_2kb_outsideCgi.region",
                        "mm9_support.15.BonaFide_CGI_Shore.cgiHunter_oe0.6_gc50_len700_2kb_outsideCgi",
                        [],
                        [],
                        None,
                        None,
                        True)
Exemplo n.º 27
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def hg18_21():
    dm.regionDatasets.update(regionDatasetsRepeatsHG18)
    dm.deriveNewDataset("hg18.21.Tandem_Repeat.tandemRepeatFinder_annotation.region",
                 "hg18_tandemRepeat",
                 [],
                 [],
                 None,
                 None,
                 True)
    dm.deriveNewDataset("hg18.21.Tandem_Repeat.tandemRepeatFinder_annotation_downsampledTo500k.region",
                 "hg18_tandemRepeat",
                 [],
                 [],
                 None,
                 None,
                 True,
                 True,
                 500000)
Exemplo n.º 28
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def mm9_21():
    dm.regionDatasets.update(regionDatasetsRepeatsMM9)
    dm.deriveNewDataset("mm9.21.Tandem_Repeat.tandemRepeatFinder_annotation.region",
                 "mm9_tandemRepeat",
                 [],
                 [],
                 "max",
                 None,
                 True)
    dm.deriveNewDataset("mm9.21.Tandem_Repeat.tandemRepeatFinder_annotation_downsampledTo500k.region",
                 "mm9_tandemRepeat",
                 [],
                 [],
                 "max",
                 None,
                 True,
                 True,
                 500000)
Exemplo n.º 29
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def mm9_27():
    dm.regionDatasets.update(regionDatasetsRepeatsMM9)
    dm.deriveNewDataset("mm9.27.Repeat_SINE.repeatMasker_annotation_short_interspersed_nucleotide_elements.region",
                        "mm9_Repeat_SINE",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True)
    dm.deriveNewDataset("mm9.27.Repeat_SINE.repeatMasker_annotation_short_interspersed_nucleotide_elements_downsampledTo500k.region",
                        "mm9_Repeat_SINE",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True,
                        500000)
Exemplo n.º 30
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def mm9_26():
    dm.regionDatasets.update(regionDatasetsRepeatsMM9)
    dm.deriveNewDataset("mm9.26.Repeat_Simple.repeatMasker_annotation_simple_repeats.region",
                        "mm9_Repeat_Simple",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True)
    dm.deriveNewDataset("mm9.26.Repeat_Simple.repeatMasker_annotation_simple_repeats_downsampledTo500k.region",
                        "mm9_Repeat_Simple",
                        [],
                        [],
                        None,
                        None,
                        True,
                        True,
                        500000)