def __process_bed(self):
bed = ReadBed(opener(self.properties['file']))
if self.properties['color'] == 'bed_rgb' and bed.file_type not in [
'bed12', 'bed9'
]:
log.warning(
"*WARNING* Color set to 'bed_rgb', but bed file does not have the rgb field. The color has "
"been set to {}".format(PlotBed.DEFAULT_COLOR))
self.properties['color'] = PlotBed.DEFAULT_COLOR
interval_tree = {}
for intval in bed:
if intval.chromosome not in interval_tree:
interval_tree[intval.chromosome] = IntervalTree()
if self.properties['color'] == 'bed_rgb':
color = intval.rgb
else:
color = self.properties['color']
interval_tree[intval.chromosome].add(
Interval(intval.start, intval.end, color))
return interval_tree
def __process_loop_file(self):
interval_tree = {}
with opener(self.properties['file']) as f:
for idx, line in enumerate(f):
line = to_string(line)
# skip header line
if idx == 0 and self.__is_header(line):
continue
fields = line.split()
chr1, x1, x2, chr2, y1, y2, *other = fields
x1, x2, y1, y2 = list(map(int, [x1, x2, y1, y2]))
# skip inter-chromosome interaction
if chr1 != chr2:
continue
chromosome = chr1
if not chromosome.startswith("chr"):
chromosome = change_chrom_names(chromosome)
if chromosome not in interval_tree:
interval_tree[chromosome] = IntervalTree()
if len(other) == 0:
color = self.DEFAULT_COLOR
else:
rgb = other[0].split(",")
rgb = list(map(int, rgb))
color = rgb2hex(*rgb)
loop = self.LoopInverval(chr1, x1, x2, chr2, y1, y2, color)
interval_tree[chromosome].add(Interval(x1, y2, loop))
return interval_tree
def __process_bed(self):
bed_file_h = ReadBed(opener(self.properties['file']))
self.bed_type = bed_file_h.file_type
if 'color' in self.properties and self.properties['color'] == 'bed_rgb' and \
self.bed_type not in ['bed12', 'bed9']:
log.warning(
"*WARNING* Color set to 'bed_rgb', but bed file does not have the rgb field. The color has "
"been set to {}".format(PlotBed.DEFAULT_COLOR))
self.properties['color'] = PlotBed.DEFAULT_COLOR
valid_intervals = 0
interval_tree = {}
max_score = float('-inf')
min_score = float('inf')
for bed in bed_file_h:
if bed.score < min_score:
min_score = bed.score
if bed.score > max_score:
max_score = bed.score
if bed.chromosome not in interval_tree:
interval_tree[bed.chromosome] = IntervalTree()
interval_tree[bed.chromosome].add(Interval(bed.start, bed.end,
bed))
valid_intervals += 1
if valid_intervals == 0:
log.warning("No valid intervals were found in file {}".format(
self.properties['file_name']))
return interval_tree, min_score, max_score