def makeWig(bamfile):
results = CLIP_analysis.get_bam_coverage(bamfile.filename)
wig = defaultdict(dict)
for step, count in results.steps():
if count > 0:
for position in step.xrange_d():
wig[step.chrom][position.pos] = count
return wig
def make_features(self):
Region = collections.namedtuple("Region", ["region", "gene_id"])
bedtracks = {}
for region in self.assigned_regions:
bedtracks[region] = pybedtools.BedTool(
os.path.join(clipper.data_dir(), "regions", "%s_%s.bed" % (self.species, region))
)
features = HTSeq.GenomicArrayOfSets("auto", stranded=True)
for region, bedtrack in bedtracks.items():
for iv, interval in izip(CLIP_analysis.bed_to_genomic_interval(bedtrack), bedtrack):
features[iv] = set([Region(region, interval.name)])
return features
def make_features(self):
Region = collections.namedtuple("Region", ["region", "gene_id"])
bedtracks = {}
for region in self.assigned_regions:
bedtracks[region] = pybedtools.BedTool(
os.path.join(clipper.data_dir(), "regions",
"%s_%s.bed" % (self.species, region)))
features = HTSeq.GenomicArrayOfSets("auto", stranded=True)
for region, bedtrack in bedtracks.items():
for iv, interval in izip(
CLIP_analysis.bed_to_genomic_interval(bedtrack), bedtrack):
features[iv] = set([Region(region, interval.name)])
return features
def get_uORF_start_stop_gff(self):
"""
Returns hg19 uORFs
"""
db = gffutils.FeatureDB(
"/nas3/yeolab/Genome/ensembl/gtf/gencode.v17.annotation.gtf.db.old"
)
transcript_gene_dict = self._create_transcript_map(db)
#get all 5' UTRs
(UTR3, UTR5, exons, genes, introns,
CDS) = CLIP_analysis.get_genomic_regions(
os.path.join(clipper.data_dir(), "regions"), "hg19", db).values()
five_prime_utr_dict = self._get_five_prime_utr_sequences(
UTR5, "/nas3/yeolab/Genome/ucsc/hg19/chromosomes/all.fa")
return self._get_uorf_start_stop(five_prime_utr_dict)
def get_uORF_start_stop_gff(self):
"""
Returns hg19 uORFs
"""
db = gffutils.FeatureDB("/nas3/yeolab/Genome/ensembl/gtf/gencode.v17.annotation.gtf.db.old")
transcript_gene_dict = self._create_transcript_map(db)
#get all 5' UTRs
(UTR3, UTR5,
exons, genes,
introns, CDS) = CLIP_analysis.get_genomic_regions(os.path.join(clipper.data_dir(), "regions"),
"hg19",
db).values()
five_prime_utr_dict = self._get_five_prime_utr_sequences(UTR5, "/nas3/yeolab/Genome/ucsc/hg19/chromosomes/all.fa")
return self._get_uorf_start_stop(five_prime_utr_dict)