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1 #!/usr/bin/env python
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2
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3
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4 class GFFLine:
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5
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6 def __init__(self, in_fields):
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7 self.seqname = in_fields[0]
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8 self.source = in_fields[1]
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9 self.feature = in_fields[2]
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10 self.start = int(in_fields[3])
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11 self.end = int(in_fields[4])
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12 self.score = in_fields[5]
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13 self.strand = in_fields[6]
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14 self.frame = in_fields[7]
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15 self.attribute = in_fields[8]
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16
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17 def __str__(self):
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18 all_atts = [
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19 self.seqname,
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20 self.source,
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21 self.feature,
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22 self.start,
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23 self.end,
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24 self.score,
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25 self.strand,
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26 self.frame,
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27 self.attribute
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28 ]
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29 all_atts = [str(i) for i in all_atts]
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30 return '\t'.join(all_atts)
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31
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32
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33 class GFFReader:
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34
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35 def __init__(self, in_gff_file):
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36 self.gff_file = in_gff_file
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37
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38 def parse_gff(self):
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39 with open(self.gff_file) as f:
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40 for line in f:
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41 if not line.startswith('#'):
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42 L1 = line.rstrip().split('\t')
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43 yield GFFLine(L1) |
