从fasta文件的标题中解析特定字符串

Question

I'm looking to obtain organism name from a fasta header file, where I'm interested in from the description to extract when OS=(Organism Name) .

FASTA 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

Code for Obtaining FastaHeader

Caenorhabditis elegans
Caenorhabditis elegans

Current Output:

 >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

Desired Output:

 Caenorhabditis elegans Caenorhabditis elegans

Answer 1

You can search for your information using a regex:

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

This Code looks for the text after "OS=" until "GN" and removes the whitespaces at the end