Parsing specific string from header from fasta file

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

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)

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

did you try regex?

Beliaev Maksim
– Beliaev Maksim

2020-09-16 14:53:29 +00:00
Commented Sep 16, 2020 at 14:53 — Beliaev Maksim
– Beliaev Maksim, Commented Sep 16, 2020 at 14:53
cross posted : biostars.org/p/461697

Pierre
– Pierre

2020-09-16 16:24:34 +00:00
Commented Sep 16, 2020 at 16:24 — Pierre
– Pierre, Commented Sep 16, 2020 at 16:24

Yannick Funk · Accepted Answer · 2020-09-16 15:02:36Z

2

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

answered Sep 16, 2020 at 15:02

Yannick Funk

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1 Comment

bioinformatics_student Over a year ago

very nice approach, thanks @yannick! :) the .start() just Return the indices of the start position where the "OS" string is correct?

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