密码子偏好性筛选序列代码

yy951010 发表于 2024-4-4 12:20

本帖最后由苏紫方璇于 2024-4-8 01:03 编辑

import os
from Bio import SeqIO
def is_valid_cds(cds):
if len(cds) <= 300:
   return False
if not (cds.startswith("ATG") and (cds.endswith("TAG") or cds.endswith("TGA") or cds.endswith("TAA"))):
   return False
if len(cds) % 3 != 0:
   return False
# 检查中间是否有终止密码子或错误碱基
for i in range(0, len(cds) - 3, 3):
   codon = cds
   if codon in ["TAG", "TGA", "TAA"] or not all(base in "ATGC" for base in codon):
         return False
return True
def filter_fasta_files(input_folder, output_folder):
if not os.path.exists(output_folder):
   os.makedirs(output_folder)

for filename in os.listdir(input_folder):
   if filename.endswith(".fasta"):
         input_path = os.path.join(input_folder, filename)
         output_path = os.path.join(output_folder, filename)

         valid_cds_records = []
         for record in SeqIO.parse(input_path, "fasta"):
            cds = str(record.seq).upper()
            if is_valid_cds(cds):
               valid_cds_records.append(record)

         SeqIO.write(valid_cds_records, output_path, "fasta")
         print(f"Filtered {len(valid_cds_records)} valid CDS sequences to {output_path}")
# 请根据你的实际情况修改这些路径
input_folder = "C:/Users/Administrator/Desktop/cds-before"# 输入文件夹的路径
output_folder = "C:/Users/Administrator/Desktop/cds-after"# 输出文件夹的路径
filter_fasta_files(input_folder, output_folder)

苏紫方璇 发表于 2024-4-8 01:03

插入代码的方法可以看这个帖子
【公告】发帖代码插入以及添加链接教程（有福利）
https://www.52pojie.cn/thread-713042-1-1.html
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密码子偏好性筛选序列代码