Mercurial > repos > dereeper > ragoo
view RaGOO/ragoo_utilities/PAFReader.py @ 13:b9a3aeb162ab draft default tip
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author | dereeper |
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date | Mon, 26 Jul 2021 18:22:37 +0000 |
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class PAFLine: """ Object to represent a single alignment in a minimap PAF file. """ def __init__(self, in_line): """ start positions should be before end positions for both query and target """ self.line = in_line.rstrip().split('\t') self.contig = self.line[0] self.query_len = int(self.line[1]) self.query_start = int(self.line[2]) self.query_end = int(self.line[3]) self.strand = self.line[4] self.ref_header = self.line[5] self.ref_len = int(self.line[6]) self.ref_start = int(self.line[7]) self.ref_end = int(self.line[8]) self.num_match = int(self.line[9]) self.aln_len = int(self.line[10]) self.mapq = int(self.line[11]) assert self.query_start <= self.query_end assert self.ref_start <= self.ref_end def __str__(self): return '\t'.join(self.line) def __eq__(self, other): return self.line == other.line class PAFReader: def __init__(self, paf_file): self.paf_file = paf_file def parse_paf(self): with open(self.paf_file) as f: for line in f: yield PAFLine(line)