2

I have the following code in python:

#/usr/bin/python

from Bio import SeqIO

count = SeqIO.convert(“genome1.gbk”, “genbank”, “genome1.fasta”, “fasta”)

print("Converted %i records" % count)

This code converts the genbank file "genome1.gbk" to a fasta file "genome1.fasta". But now I want to convert all files in the current folder with this code. All the files in the current folder are genbank files and I want them to turn into fasta files with this code. I was thinking of using wildcards, but I don't know exactly how to change this code. Any help is appreciated

  • Are there nested folders with files? – RomanPerekhrest Nov 26 '19 at 17:31
  • Nope, only genbank files. – tucanco Nov 26 '19 at 18:46
0

With Python's os.scandir feature:

#/usr/bin/python

from Bio import SeqIO
from os import scandir

with scandir() as it:
    for entry in it:
        if entry.name.endswith('.gbk') and entry.is_file():
            count = SeqIO.convert(entry.name, 'genbank', '{}.fasta'.format(entry.name[:-4]), 'fasta')
            print("Converted %i records" % count)
  • 1
    it worked wonderfully !! – tucanco Nov 26 '19 at 20:11
0

You may follow this code:

import os 
from Bio import SeqIO

for filename in os.listdir('.'):
  if filename.endswith(".gbk"):
    count = SeqIO.convert(filename, “genbank”, "{}.fasta".format(entry.name[:-4]), “fasta”)
    print("Converted %i records" % count)

BR,
Shahar

  • But in this case, all the outputs would have the same name (genome1.fasta) I'm right?. This code overwrite the output files with the same name and I don't want that. All the output files must have the same input names, but instead .gbk it must be .fasta – tucanco Nov 26 '19 at 19:06
  • OK, got it, fixed my answer – Shahar Gino Nov 29 '19 at 12:15

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