assembly = a
UPSTREAM_PROMOTOR_DIST = 2000
DOWNSTREAM_PROMOTOR_DIST = 2000
writer = csv.writer(open(outfile, "w"), delimiter="\t")
genome = Genome(assembly)
###
# load data
genedata = Ensembl.EnsemblGenes(assembly=assembly)
genes = Ensembl.ReverseGeneMapping(genedata)
genespluspromotor = Ensembl.ReverseGeneMapping(
genedata, tssPadding=UPSTREAM_PROMOTOR_DIST)
genepromotors = Ensembl.ReversePromotorMapping(
genedata,
upstreamPadding=UPSTREAM_PROMOTOR_DIST,
downstreamPadding=DOWNSTREAM_PROMOTOR_DIST)
exons = Ensembl.ReverseExonMapping(genedata)
transcriptionSites = Ensembl.TranscriptionSites(genedata)
# UCSC table browser - Expression & Regulation - CpG Islands
# Download all columns with exception of "bin"
writer = csv.writer(open(outfile, "w"), delimiter="\t")
###
TSS_TTS_Distance = 5000
TTS_TTS_Distance_Human = str(TSS_TTS_Distance / 1000) + "kb"
Small_TSS_TTS_Distance = 1000
Small_TTS_TTS_Distance_Human = str(Small_TSS_TTS_Distance / 1000) + "kb"
# load data
genedata = Ensembl.EnsemblGenes(assembly="hg18", annotation="ncbi36.1")
genes = Ensembl.ReverseGeneMapping(genedata)
exons = Ensembl.ReverseExonMapping(genedata)
transcriptionSites = Ensembl.TranscriptionSites(genedata)
cpgIslands = ExtendedBed(
os.path.expanduser(
"~/mount/publicdata/hg18/cpgislands/cpgislands-0-index.bed"))
affyannotation = NetAffxAnnotation()
paddedGenes = Ensembl.ReverseGeneMapping(genedata, tssPadding=TSS_TTS_Distance)
def isUpstream(distance, strand):