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13
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1 class PAFLine:
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2 """ Object to represent a single alignment in a minimap PAF file. """
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3
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4 def __init__(self, in_line):
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5 """
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6 start positions should be before end positions for both query and target
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7 """
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8 self.line = in_line.rstrip().split('\t')
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9 self.contig = self.line[0]
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10 self.query_len = int(self.line[1])
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11 self.query_start = int(self.line[2])
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12 self.query_end = int(self.line[3])
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13 self.strand = self.line[4]
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14 self.ref_header = self.line[5]
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15 self.ref_len = int(self.line[6])
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16 self.ref_start = int(self.line[7])
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17 self.ref_end = int(self.line[8])
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18 self.num_match = int(self.line[9])
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19 self.aln_len = int(self.line[10])
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20 self.mapq = int(self.line[11])
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21
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22 assert self.query_start <= self.query_end
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23 assert self.ref_start <= self.ref_end
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24
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25 def __str__(self):
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26 return '\t'.join(self.line)
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27
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28 def __eq__(self, other):
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29 return self.line == other.line
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30
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31
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32 class PAFReader:
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33
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34 def __init__(self, paf_file):
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35 self.paf_file = paf_file
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36
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37 def parse_paf(self):
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38 with open(self.paf_file) as f:
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39 for line in f:
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40 yield PAFLine(line) |
