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#!/usr/bin/env python3
class RoiRecord(object):
"""Represent one record in a ROI file."""
def __init__(self, ref, start_pos, end_pos, region_name, region_length,
strand, max_count, data, points):
"""Initialize RoiRecord."""
self.ref = ref
self.start_pos = start_pos
self.end_pos = end_pos
self.strand = strand
self.region_length = region_length
self.region_name = region_name
self.max_count = max_count
self.data = data
self.points = points
def __str__(self):
return 'RoiRecord(%s, %s, %s, %s, %s, %s, %s, %s, len([...])==%s)' % \
(repr(self.ref), self.start_pos, self.end_pos,
self.region_name, self.region_length, repr(self.strand),
self.max_count, self.data, len(self.points))
def __repr__(self):
return self.__str__()
def loadRoi(path, max_count=0):
"""Load ROI file and return it as a list of RoiRecord objects.
NA values are translated to 0.
"""
data_keys = []
result = []
i = 0
with open(path, 'rb') as f:
for line in f:
if line.startswith('##'):
data_keys = line[2:].split('\t')[7:-1]
if line[0] == '#':
continue
if max_count > 0 and i >= max_count:
break
i += 1
vals = line.split()
region_length = int(vals[4])
data = vals[7:-1]
points = [int(x) for x in vals[-1].split(',')]
r = RoiRecord(vals[0], int(vals[1]) - 1, int(vals[2]), vals[3],
region_length, vals[5], int(vals[6]), data, points)
result.append(r)
#print ' => Loaded %d records.' % len(result)
return data_keys, result
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