Python：如何根据位置输出FASTAheader或染色体索引图？

Question

我有代码可以帮助我在大小为 5 的 window 从左向右移动时移动它。该文件采用 fasta 格式，例如 header >chromosome 后跟染色体索引。我想根据确切的索引输出 header 索引号。谁能帮帮我？

代码

from Bio import SeqIO

with open("test1_out.fasta","w") as f:
        for seq_record in SeqIO.parse("test1.fasta", "fasta"):
            for i in range(len(seq_record.seq) - 4) :
               f.write(">" + str(seq_record.id) + "\n")
               f.write(str(seq_record.seq[i:i+5]) + "\n")

test1.fasta

>chr1:1-8 
ATCGCGTC
>chr2:1-10
ATTTTCGCGA

实际产量

>chr1:1-8
ATCGC
>chr1:1-8
TCGCG
>chr1:1-8
CGCGT
>chr1:1-8
GCGTC
>chr2:1-10
ATTTT
>chr2:1-10
TTTTC
>chr2:1-10
TTTCG
>chr2:1-10
TTCGC
>chr2:1-10
TCGCG
>chr2:1-10
CGCGA

期望输出

>chr1:1-5
ATCGC
>chr1:2-6
TCGCG
>chr1:3-7
CGCGT
>chr1:4-8
GCGTC
>chr2:1-5
ATTTT
>chr2:2-6
TTTTC
>chr2:3-7
TTTCG
>chr2:4-8
TTCGC
>chr2:5-9
TCGCG
>chr2:6-10
CGCGA

Answer 1

你只需要修改标题写法：

seq_name = seq_record.id.split(":")[0]  # Get the "chr1"
for i in range(len(seq_record.seq) - 4):        
    seq_coords = "{}-{}".format(i + 1, i + 5)  # Make the coordinates

    f.write(">" + seq_name + ":" + seq_coords + "\n")  # Print them both

Python：如何根据位置输出FASTAheader或染色体索引图？

Python: How to output the FASTA header or chromosome index figure according to the location?

python

loops

bioinformatics

fasta

biopython