python：计算fasta的GC含量

导读

用python3脚本统计fasta文件碱基数、GC含量

python3脚本

fasta文件、格式就不多说了

#usr/bin/env python3
import os,sys,re
ms, infile, outfile = sys.argv
with open(infile) as f:
    f=f.read()  
    # read()将整个文件读到内存
    f=re.sub('>.*\n|\n', '', f)
    # 去掉标题行、回车符
    size=len(f)
    nG=f.count("g")+f.count("G")
    nC=f.count("c")+f.count("C")
    percent_GC=(nG+nC)/size
with open(outfile, 'w') as out:
    out.write("ID\tsize\tpercent_gc\n")
    ID=re.sub('.fasta', '', infile)
    out.write("{}\t{}\t{}\n".format(ID, size, percent_GC))
    # 行末尾加\n

运行，计算碱基数、GC含量

python3 assembly.fasta out.file
# 使用python3 infile outfile

结果