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class Error (Exception): pass
class Snp:
def __init__(self, line):
#[P1] [SUB] [SUB] [P2] [BUFF] [DIST] [LEN R] [LEN Q] [FRM] [TAGS]
#187 A C 269 187 187 654 853 1 1 ref_name qry_name
try:
l = line.rstrip().split('\t')
self.ref_pos = int(l[0]) - 1
self.ref_base = l[1]
self.qry_base = l[2]
self.qry_pos = int(l[3]) - 1
self.ref_length = int(l[6])
self.qry_length = int(l[7])
self.ref_name = l[10]
self.qry_name = l[11]
except:
raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
def __eq__(self, other):
return type(other) is type(self) and self.__dict__ == other.__dict__
def __str__(self):
return '\t'.join([str(x) for x in [
self.ref_pos + 1,
self.ref_base,
self.qry_base,
self.qry_pos + 1,
self.ref_length,
self.qry_length,
self.ref_name,
self.qry_name
]])
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