Created
May 4, 2016 04:25
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Blast parser
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class BlastOut(object): | |
def __init__(self, line): | |
col = line.strip().split() | |
self.col_string = line.strip() | |
self.q = col[0] | |
self.s = col[1] | |
self.identity = float(col[2]) | |
self.alignment_len = int(col[3]) | |
self.mismatches = int(col[4]) | |
self.gap_open = int(col[5]) | |
self.q_start = int(col[6]) | |
self.q_end = int(col[7]) | |
self.s_start = int(col[8]) | |
self.s_end = int(col[9]) | |
self.e_value = float(col[10]) | |
self.bit = float(col[11]) | |
self.primary_key = uuid.uuid4().hex | |
self.q_pair = (self.q_start, self.q_end) | |
self.s_pair = (self.s_start, self.s_end) | |
if abs(self.q_start - self.q_end) < abs(self.s_start - self.s_end): | |
self.pairs = [self.s_pair, self.q_pair] | |
else: | |
self.pairs = [self.q_pair, self.s_pair] | |
def __str__(self): | |
return "query: %s, subject: %s" % (self.q, self.s) | |
class BlastIter(object): | |
def __init__(self, _file): | |
self.file = _file | |
def __iter__(self): | |
with open(self.file, "r") as f: | |
for line in f: | |
yield BlastOut(line) | |
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it can be used as follows: