从 fasta 文件中解析 header 中的特定字符串

Question

我想从 fasta header 文件中获取有机体名称，我感兴趣的是从描述中提取什么时候 OS=(有机体名称) .

法斯塔 HEADER

>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

FastaHeader获取代码

from Bio import SeqIO
import re
import pandas as pd


input_file = "ANIMAL.fasta" 

fasta_sequences = SeqIO.parse(open(input_file),'fasta')
for fasta in fasta_sequences:
    fasta_id, sequence = fasta.id, str(fasta.seq)
    print(fasta.description)

当前输出：

>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

期望的输出：

Caenorhabditis elegans
Caenorhabditis elegans

Answer 1

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

从 fasta 文件中解析 header 中的特定字符串

Parsing specific string from header from fasta file

python

bioinformatics

biopython

fasta