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1 #!/usr/bin/env python
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2
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3 class RoiRecord(object):
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4 """Represent one record in a ROI file."""
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5
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6 def __init__(self, ref, start_pos, end_pos, region_name, region_length,
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7 strand, max_count, data, points):
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8 """Initialize RoiRecord."""
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9 self.ref = ref
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10 self.start_pos = start_pos
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11 self.end_pos = end_pos
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12 self.strand = strand
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13 self.region_length = region_length
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14 self.region_name = region_name
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15 self.max_count = max_count
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16 self.data = data
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17 self.points = points
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18
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19 def __str__(self):
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20 return 'RoiRecord(%s, %s, %s, %s, %s, %s, %s, %s, len([...])==%s)' % \
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21 (repr(self.ref), self.start_pos, self.end_pos,
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22 self.region_name, self.region_length, repr(self.strand),
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23 self.max_count, self.data, len(self.points))
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24 def __repr__(self):
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25 return self.__str__()
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26
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27
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28 def loadRoi(path, max_count=0):
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29 """Load ROI file and return it as a list of RoiRecord objects.
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30
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31 NA values are translated to 0.
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32 """
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33 data_keys = []
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34 result = []
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35 i = 0
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36 with open(path, 'rb') as f:
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37 for line in f:
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38 if line.startswith('##'):
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39 data_keys = line[2:].split('\t')[7:-1]
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40 if line[0] == '#':
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41 continue
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42 if max_count > 0 and i >= max_count:
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43 break
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44 i += 1
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45 vals = line.split()
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46 region_length = int(vals[4])
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47 data = vals[7:-1]
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48 points = [int(x) for x in vals[-1].split(',')]
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49 r = RoiRecord(vals[0], int(vals[1]) - 1, int(vals[2]), vals[3],
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50 region_length, vals[5], int(vals[6]), data, points)
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51 result.append(r)
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52 #print ' => Loaded %d records.' % len(result)
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53 return data_keys, result
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