def add_region(self, region):
"""
Add region to the class.
"""
# Parse the region length
if region not in self.region_lens:
chrom, start, end, strand = utils.parse_coords(region)
region_len = end - start + 1
# Record region length
self.region_lens[region] = region_len
# Record number of counts per region
self.region_counts[region] += 1
def add_region(self, region):
"""
Add region to the class.
"""
# Parse the region length
if region not in self.region_lens:
chrom, start, end, strand = utils.parse_coords(region)
region_len = end - start + 1
# Record region length
self.region_lens[region] = region_len
# Record number of counts per region
self.region_counts[region] += 1
def get_3p_to_5p(self):
"""
Get 3' UTR to 5' UTR ratio: Computed at the transcript level.
"""
for transcript in self.region_counts_by_transcript:
transcript_info = self.region_counts_by_transcript[transcript]
# Skip transcripts that don't have 3p / 5p UTR reads
if (len(transcript_info["3p_utr"]) == 0) or (len(transcript_info["5p_utr"]) == 0):
continue
# Take sum of 3p UTR reads and their length
sum_reads_3p = 0
sum_lens_3p = 0
for region in transcript_info["3p_utr"]:
chrom, start, end, strand = utils.parse_coords(region)
num_reads = transcript_info["3p_utr"][region]
curr_len = end - start + 1
sum_reads_3p += num_reads
sum_lens_3p += curr_len
# Take sum of 5p UTR reads and their lengths
sum_reads_3p = [transcript_info["3p_utr"][r] for r in transcript_info["3p_utr"]]
return 0
def get_3p_to_5p(self):
"""
Get 3' UTR to 5' UTR ratio: Computed at the transcript level.
"""
for transcript in self.region_counts_by_transcript:
transcript_info = \
self.region_counts_by_transcript[transcript]
# Skip transcripts that don't have 3p / 5p UTR reads
if (len(transcript_info["3p_utr"]) == 0) or \
(len(transcript_info["5p_utr"]) == 0):
continue
# Take sum of 3p UTR reads and their length
sum_reads_3p = 0
sum_lens_3p = 0
for region in transcript_info["3p_utr"]:
chrom, start, end, strand = utils.parse_coords(region)
num_reads = transcript_info["3p_utr"][region]
curr_len = end - start + 1
sum_reads_3p += num_reads
sum_lens_3p += curr_len
# Take sum of 5p UTR reads and their lengths
sum_reads_3p = [transcript_info["3p_utr"][r] \
for r in transcript_info["3p_utr"]]
return 0
