2

我有以下代码：

from Bio import AlignIO
import itertools

out=open("test.csv","a")
align = AlignIO.read("HPV16_CG.aln.fas", "fasta")
n=0
def SNP(line):  
    result=[]
    result.append(str(n+1))
    result.append(line[0])
    result.append(align[y].id.rsplit("|")[3])
    result.append(x)
    return result



while n<len(align[0]):
  line = align[:,n]
  y=0
  for x in line:
    if line[0]!=x:
      print >> out, ','.join(map(str,SNP(line)))
      y=y+1
    else:
      y=y+1
  y=0
  n=n+1
out.close()

f=open("test.csv","rU")

out=open("test_2.csv","a")
lines=f.read().split()

for key, group in itertools.groupby(lines, lambda line: line.partition(',')[0]):
    print >>out, ','.join(group)

out.close()
f.close()

如您所见，我目前正在编写两个文件。我真的只需要第二个文件。有没有人有任何建议将两个“下标”合并为一个？

输入文件“HPV16_CG.aln.fas”如下所示：

>gi|333031|lcl|HPV16REF.1| Alpha-9 - Human Papillomavirus 16, complete genome. 
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG

>gi|333031|gb|K02718.1|PPH16 Human papillomavirus type 16 (HPV16), complete genome
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG

>gi|196170262|gb|FJ006723.1| Human papillomavirus type 16, complete genome
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG

我非常感谢所有帮助/建议来帮助我改进这一点！

4

1 回答 1

1

最简单的做法是将文件的行保留在内存中，但我怀疑这不会起作用，因为任何有用的生物信息学文件都可能非常大。

这是通过删除全局变量使用并添加生成器函数来以流方式创建从函数返回的行来清理脚本的尝试，这些行SNP应该与您的itertools.groupby调用兼容。

from Bio import AlignIO
import itertools

n=0
align = AlignIO.read("HPV16_CG.aln.fas", "fasta")

def SNP(line, y, x):
    """Pass y as a parameter rather than relying on a global"""  
    result=[]
    result.append(str(n+1))
    result.append(line[0])
    result.append(align[y].id.rsplit("|")[3])
    result.append(x)
    return result

def generate_snp_lines(align, n):
    """this is a function generator that'll produce lines without writing them to a file"""
    while n<len(align[0]):
        line = align[:,n]
        y=0
        for x in line:
            if line[0]!=x:
                yield ','.join(map(str,SNP(line, y, x)))
            y+=1
        n+=1

def main():

    # let's use a context manager to open and cleanup this file for us:
    with open("test.csv","a") as out:
        # construct the generator:
        lines = generate_snp_lines(align, n)
        # pass it to itertools.groupby like we'd pass any iterable:
        for key, group in itertools.groupby(lines, lambda line: line.partition(',')[0]):
            print >>out, ','.join(group)

if __name__=="__main__":
    main()
于 2012-08-05T15:33:14.687 回答