[英]How to find identical sequences in Python
我是Python的新手,我想知道如何從Python中的Fasta文件中查找相同的序列。 例如,在這里我有4個記錄序列讀取,如何找到相同的序列並返回其ID? 非常感謝你!!
from Bio import SeqIO
record=list(SeqIO.parse("data/dna.txt", "fasta"))
for i in range(0,len(record)):
print record[i].id,record[i].seq
seq1 GAATGCATACTGCATCGATA
seq2 CATAAAACGTCTCCATCGCT
seq3 TGCCCAAGTTGTGAAGTGTC
seq4 TGCCCAAGTTGTGAAGTGTC
您可以使用defaultdict
編譯每個序列的ID列表,如下所示:
from Bio import SeqIO
from collections import defaultdict
records=list(SeqIO.parse("data/dna.txt", "fasta"))
compilation = defaultdict(list)
for record in records:
compilation[record.seq].append(record.id)
最簡單的方法是使用dict
。
from Bio import SeqIO
records = list(SeqIO.parse("data/dna.txt", "fasta"))
d = dict()
for record in records:
if record.seq in d:
d[record.seq].append(record)
else:
d[record.seq] = [record]
for seq, record_set in d.iteritems():
print seq + ': (' + str(len(record_set)) + ')'
for record in record_set:
print ' ' + record.id
打印像:
GAATGCATACTGCATCGATA: (1)
seq1
CATAAAACGTCTCCATCGCT: (1)
seq2
TGCCCAAGTTGTGAAGTGTC: (2)
seq3
seq4
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