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)
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)
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)
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)
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)
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)
def mm9_16():
dm.extractFlanks("mm9.5.BonaFide_CGI.cgiHunter_oe0.6_gc50_len700.region",
"mm9_support.16.500bp_centered_downstream",
False,"start",
# 250,"int(min(250,(chromend-chromstart)*0.25))")
250,250)
dm.extractFlanks("mm9.5.BonaFide_CGI.cgiHunter_oe0.6_gc50_len700.region",
"mm9_support.16.500bp_centered_upstream",
False,"end",
# "int(min(250,(chromend-chromstart)*0.25))",250)
250,250)
dm.mergeDatasets("mm9_support.16.BonaFide_CGI_Border.cgiHunter_oe0.6_gc50_len700_500bp_centeredOnBorders",
["mm9_support.16.500bp_centered_downstream",
"mm9_support.16.500bp_centered_upstream"])
dm.deriveNewDataset("mm9.16.BonaFide_CGI_Border.cgiHunter_oe0.6_gc50_len700_500bp_centeredOnBorders.region",
"mm9_support.16.BonaFide_CGI_Border.cgiHunter_oe0.6_gc50_len700_500bp_centeredOnBorders",
[],
[],
"max",
None,
True)
def hg18_12_new():
dm.extractFlanks("hg18_support.12.DNaseI_HS_site.hg18_tCell_DNaseI_hypersensitive_sites_Boyle2008",
"hg18_support.12.DNaseI_HS_site.hg18_tCell_DNaseI_hypersensitive_sites_Boyle2008_1kb",
False,"whole_region",
"max(0,int(500-(chromend-chromstart)/2))","max(0,int(500-(chromend-chromstart)/2))")
dm.regionDatasets.update(regionDatasets_DNaseI_Duke)
dm.mergeDatasets("hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged",regionDatasets_DNaseI_Duke.keys())
dm.extractFlanks("hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged",
"hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged_1kb",
False,"whole_region",
"max(0,int(500-(chromend-chromstart)/2))","max(0,int(500-(chromend-chromstart)/2))")
dm.regionDatasets.update(regionDatasets_DNaseI_Washington)
dm.mergeDatasets("hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged",
regionDatasets_DNaseI_Washington.keys())
dm.extractFlanks("hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged",
"hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged_1kb",
False,"whole_region",
"max(0,int(500-(chromend-chromstart)/2))","max(0,int(500-(chromend-chromstart)/2))")
# datasetCurrent = {"hg18_support.12.DNaseI_HS_site.hg18_tCell_DNaseI_hypersensitive_sites_Boyle2008_1kb":defaultFolder+"hg18_support.12.DNaseI_HS_site.hg18_tCell_DNaseI_hypersensitive_sites_Boyle2008_1kb"+".txt",
# "hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged_1kb":defaultFolder+"hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged_1kb"+".txt",
# "hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged_1kb":defaultFolder+"hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged_1kb"+".txt",
# }
# dm.regionDatasets.update(datasetCurrent)
dm.mergeDatasets("hg18_support.12.All_DNaseI_datasets_merged",
["hg18_support.12.DNaseI_HS_site.hg18_tCell_DNaseI_hypersensitive_sites_Boyle2008_1kb",
"hg18_support.12.Duke_GM12878_HelaS3_K562_hepg2_SortedNotMerged_1kb",
"hg18_support.12.Open_Chromatin.ENCODE_DNaseI_hypersensitive_sites_SortedNotMerged_1kb"
])
dm.deriveNewDataset("hg18.12_new.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)
def mm9_18():
dm.extractFlanks("mm9_imprintedGenes",
"mm9.18.Imprinted_Promoter.Promoter_region_refSeqGenesMinus10000ToPlus2000AroundTSS_otagoList.region",
True,"start",10000,2000)
