替换dna序列文件中特定位置的核苷酸

Question

我有一个fasta文件，另一个文件包含位置，我想用默认设置替换每个序列的某个位置，例如，我的位置文件看起来像a / c 120，我的替换表看起来像a / c到W，所以我想获得一个新的fasta文件，位置120替换为w。

该程序是用Python编写的

因此，第一个问题是我无法到达正确的位置，例如，如果我使用my_seq_id [0：3]，则会得到序列名称！ 不是顺序。 位置文件看起来像id1 219 A / C

from Bio import SeqIO
import sys
import string
userInput1=raw_input("enter your sequence:")
userInput2=raw_input('enter your position file:')
fasta_file=userInput1
position_file=userInput2
result_file="outfile.txt"
id_list=list()
position_list=list()
nucleotide_list=list()
with open(position_file) as f:
    for line in f:
        line=line.strip()
        headerline = line.split()
        position=headerline[1]
        ID=headerline[0]
        nucleotide=headerline[2]
        nucleotide_list.add(nucleotide)
        position_list.add(position)
        id_list.add(ID)
fasta_sequence=SeqIO.parse(open(fasta_file), 'fasta')
with open(result_file, 'w') as f:
    if seq_record.id in wanted and nucleotide_list="A/C":
        seq_record[position_list]="W\n"
        SeqIO.write([seq_record], f, "fasta")

Answer 1

您的代码有些混乱，不应：

fasta_sequence=SeqIO.parse(open(fasta_file), 'fasta')
with open(result_file, 'w') as f:
    if seq_record.id in wanted and nucleotide_list="A/C":
        seq_record[position_list]="W\n"
        SeqIO.write([seq_record], f, "fasta")

是：

fasta_sequence=SeqIO.parse(open(fasta_file), 'fasta')
with open(result_file, 'w') as f:
    if fasta_sequence[j].id in wanted and nucleotide_list[i]=="A/C":
        fasta_sequence[j].seq[position_list]="W\n"
        SeqIO.write([fasta_sequence[j]], f, "fasta")

作为我的计数器来通过nucleotide_list和j来通过fasta_sequence

您还可以执行以下操作，通过fasta_sequence进行迭代：

for record in SeqIO.parse(StringIO(data), "fasta"):
    print("%s %s" % (record.id, record.seq))

作为id每个元素的id并按顺序排列。

----更新----

我想我了解您想要做什么，请检查文件中的每个记录，检查id是否匹配，然后在该位置更改顺序：

#goes through each record in the file
for record in SeqIO.parse(StringIO(data), "fasta"):
    # check if id is wanted
    if record.id in id_list:
        # get list of every item in id_list that matches record.id
        positions_of_id_in_id_list = [i for i, j in enumerate(id_list) if j == record.id]
        for elem_position_lists in positions_of_id_in_id_list:
            # I think here you want to write the new record in the correct position (substitute "W\n" with new item. Maybe nucleotide[elem_position_lists]?)
            record.seq[position_list[elem_position_lists]] = "W\n"
# write new file
SeqIO.write(fasta_sequence, f, "fasta")