splitting multifasta-file in python

Question

[twesigomwedavid]

Hello,

How can I split a multi-fasta file into individual sequence files in python?

[Bastien Hervé]

Always show an attempt in your post to show you tried something first.

Some hints :

• You can use Biopython but it can be slow if you have a huge file

• Or read the file line by line in a for loop, for each ">" at the beginning of a line, create a new file and write the current line and the next one into it. (you can even use the header of each sequence as output file name)

I think you can even do that in one Unix command

[twesigomwedavid]

Okay, thank you Bastien

[GenoMax]

If this is a assignment you should always show the code your have written so far (if you need specific help).

Otherwise there are similar questions/solutions that can be found on this forum. Try doing an external google search.

Answer 1

[Joe]

As the others have said, see other results on this forum, for example: Split the multiple sequences file into a separate files

Answer 2

[Siya Diya]

Try this code

#!/usr/bin/env python
import os
from Bio import SeqIO
def split(fastafile     =   "test_fasta.fasta",
          outfastadir   =   "splitoutput"):
    """Extract multiple sequence fasta file and write each sequence in separate file"""
    os.system("mkdir -p %s"% (outfastadir))
    with open (fastafile) as FH:
        record          =   SeqIO.parse(FH, "fasta")
        file_count      =   0
        for seq_rec in record:
            file_count  =   file_count  +   1
            with open("%s/%s.fasta" % (outfastadir,str(file_count)), "w") as FHO:
                SeqIO.write(seq_rec, FHO, "fasta")
    if file_count       == 0:
        raise Exception("No valid sequence in fasta file")
    return "Done"

if __name__ == '__main__':
    import argparse
    parser = argparse.ArgumentParser(version="1.0",
                                     description="Extract multiple sequence fasta file and write each sequence in separate file")

    parser.add_argument('-f','--fastafile',
                        action  ="store",
                        default ="test_fasta.fasta",
                        help="Fasta File for parsing")
    parser.add_argument('-d','--outfastadir',
                        action  ="store",
                        default ="splitoutput",
                        help    ="Fasta File output directory")

    args = parser.parse_args()
    split(fastafile     =   args.fastafile,
          outfastadir   =   args.outfastadir)

[Ahmed Ezat El Zowalaty]

Not working unfortunately

[Joe]

You need to be more specific in the manner in which it is not working if you desire further help.

[lachiemck]

I had a similar problem, and got this from another user on here (a.zielezinski)

d={}
fh = open("sequence.fa", "r")
for seq_record in SeqIO.parse(fh, "fasta"):
     species_name = seq_record.id.split('-')[-1]
     if species_name not in d:
         d[species_name] = open(f"{species_name}.fa", "w")
     d[species_name].write(seq_record.format("fasta"))

fh.close()

Here's a link to my thread I got given it in Sorting and writing multifasta entries to new fasta files