[英]Parsing specific string from header from fasta file
我希望从 fasta 头文件中获取生物体名称,我感兴趣的是从描述中提取OS=(Organism Name)时提取的名称。
快速头>sp|Q8T8B9|ACMSD_CAEEL 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase OS=Caenorhabditis elegans GN=acsd-1 PE=2 SV=1 MPICEFSATSKSRKIDVHAHVLPKNIPDFQEKFGYPGFVRLDHKEDGTTHMVKDGKLFRV VEPNCFDTETRIADMNRANVNVQCLSTVPVMFSYWAKPADTEIVARFVNDDLLAECQKFP GKEHIVLGTDYPFPLGEL EVGRVVEEYKPFSAKDREDLLWKNAVKMLDIDENLLFNKDF >sp|P34455|ACON_CAEEL Probable aconitate hydratase, mitochondrial OS=Caenorhabditis elegans GN=aco-2 PE=3 SV=2 MNSLLRLSHLAGPAHYRALHSSSSIWSKVAISKFEPKSYLPYEKLSQTVKIVKDRLKRPL TLSEKILYGHLDQPKTQDIERGVSYLRLRPDRVAMQDATAQMAMLQFISSGLPKTAVPST IHCDHLIEAQKGGAQDLARAKDLNKEVFNFLATAGSKYGVGFWKPGSGIIHQIILENYAF
获取 FastaHeader 的代码
Caenorhabditis elegans
Caenorhabditis elegans
电流输出:
>sp|Q8T8B9|ACMSD_CAEEL 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase OS=Caenorhabditis elegans GN=acsd-1 PE=2 SV=1 >sp|P34455|ACON_CAEEL Probable aconitate hydratase, mitochondrial OS=Caenorhabditis elegans GN=aco-2 PE=3 SV=2
期望输出:
Caenorhabditis elegans Caenorhabditis elegans
您可以使用正则表达式搜索您的信息:
import re
example = "sp|P34455|ACON_CAEEL Probable aconitate hydratase, mitochondrial OS=Caenorhabditis elegans GN=aco-2 PE=3 SV=2"
start = re.search("OS", example).start()
result = example[start+3:].split("GN")[0].strip()
print(result)
>> Caenorhabditis elegans
此代码查找“OS =”之后的文本,直到“GN”并删除末尾的空格
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