Source code for hit

[docs]class HIT:
[docs] def __init__(self, seq_record, start, end, strand, score, tffm_name, tffm_matched_state): # start and end are 1-based self.seq_record = seq_record self.start = start self.end = end self.strand = strand self.score = score self.tffm_matched_state = tffm_matched_state self.tffm_name = tffm_name
[docs] def __len__(self): return self.end - self.start + 1
[docs] def __str__(self): string = "%s\t%d\t%d\t%s\t%s\t%s\t%d\t%s"%(self.seq_record.id, self.start, self.end, self.strand, self.sequence(), self.tffm_name, self.tffm_matched_state, repr(self.score)) return string
[docs] def __lt__(self, other): if other: return self.score < other.score else: return False
[docs] def __le__(self, other): if other: return self.score <= other.score else: return False
[docs] def __eq__(self, other): if other: return self.score == other.score else: return False
[docs] def __ne__(self, other): if other: return self.score != other.score else: return True
[docs] def __gt__(self, other): if other: return self.score > other.score else: return True
[docs] def __ge__(self, other): if other: return self.score >= other.score else: return True
[docs] def sequence(self): seq = self.seq_record.seq[self.start-1:self.end] if self.strand == "+": return seq else: return seq.reverse_complement()