假设我有一个包含 3 个序列的 fasta ......
ATTTTTGGA
AT
A
我希望我的序列数据如下所示:
ATTTTTGGA
ATTNNNNNN
ANNNNNNNN
是否有任何程序或脚本可以在合理的时间范围内完成此任务。我有成千上万的序列。谢谢!
我在胡闹并尝试过这个,文件最终是空白的,但这是我得到的。
import sys
from Bio import SeqIO
from Bio.Seq import Seq
in_file = open(sys.argv[1],'r')
sequences = SeqIO.parse(in_file, "fasta")
output_in_file = open("test.fasta", "w")
for record in sequences:
n = 150
record.seq = record.seq + ("N" * n)
seq = seq[:n]
output_in_file.close()
in_file.close()
最佳答案
改进你的代码,
import sys
from Bio import SeqIO
from Bio.Seq import Seq
with open(sys.argv[1], "r") as in_file:
sequences = list(SeqIO.parse(in_file, "fasta"))
n = max(map(len, sequences)) #find max len in sequences
for record in sequences:
record.seq = record.seq + ("N" * (n-len(record)))
SeqIO.write(sequences, "test.fasta", "fasta")
你得到,在
test.fasta
>id_1 ATTTTTGGA >id_2 ATNNNNNNN >id_3 ANNNNNNNN
for "all equal 150bp"
import sys
from Bio import SeqIO
from Bio.Seq import Seq
with open(sys.argv[1], "r") as in_file:
sequences = list(SeqIO.parse(in_file, "fasta"))
n = 150
for record in sequences:
record.seq = record.seq + ("N" * (n-len(record)))
SeqIO.write(sequences, "test.fasta", "fasta")
你得到,
>id_1
ATTTTTGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>id_2
ATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>id_3
ANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
关于bioinformatics - 将 Ns 添加到可变长度序列以使它们都等于 150bp 的最快方法,我们在Stack Overflow上找到一个类似的问题: https://stackoverflow.com/questions/42429295/