Pull out fastas from a multifasta based on keyword search as a string or keyfile

fastafetcher.py

# Extract fasta files by their descriptors stored in a separate file.
# Requires biopython

from Bio import SeqIO
import sys
import argparse

def getKeys(args):
	"""Turns the input key file into a list. May be memory intensive."""

	with open(args.keys, "r") as kfh:
		keys = []
    		for line in kfh:
			line = line.rstrip('\n')
			line = line.lstrip('>')
			keys.append(line)

	return keys

def main():
	"""Takes a string or list of strings in a text file (one per line) and retreives them and their sequences from a provided multifasta."""
	# Parse arguments from the commandline:
	try:
   		parser = argparse.ArgumentParser(description='Retrieve one or more fastas from a given multifasta.')
		parser.add_argument(
			'-f',
			'--fasta',
			action='store',
			required=True,
			help='The multifasta to search.')
		parser.add_argument(
			'-k',
			'--keys',
			action='store',
			required=True,
			help='A string provided directly, or a file of header strings to search the multifasta for. Must be exact. Must be one per line.')
		parser.add_argument(
			'-o',
			'--outfile',
			action='store',
			default=None,
			help='Output file to store the new fasta sequences in. Just prints to screen by default.')
		parser.add_argument(
			'-v',
			'--verbose',
			action='store_true',
			help='Set whether to print the key list out before the fasta sequences. Useful for debugging.')
		parser.add_argument(
			'-i',
			'--invert',
			action='store_true',
			help='Invert the search, and retrieve all sequences NOT specified in the keyfile.')
		args = parser.parse_args()
	
	except:
		print('An exception occured with argument parsing. Check your provided options.')
		sys.exit(1)
# Main code:
	# Call getKeys() to create the list of keys from the provided file:
	try:
		keys = getKeys(args.keys)
	
	# If -k/--keys was provided with a string, not a file path, the IO error is used as the indicator
	# to switch to expecting a string only, rather than a file.
	except IOError:
		keys = args.keys
	else:
		print("Couldn't determine a key from your provided file or string. Double check your file, or ensure your string is quoted correctly.")

	if args.verbose is not False:
		if args.invert is False:
			print('Fetching the following keys from: ' + inFile)
			for key in keys:
				print(key)
		else:
			print('Ignoring the following keys, and retreiving everything else from: ' + inFile)
			for key in keys:
				print(key)

	# Parse in the multifasta and assign an iterable variable:
        seqIter = SeqIO.parse(inFile, 'fasta')

	# For each sequence in the multifasta, check if it's in the keys[] tuple. If so, print it out:
	for seq in seqIter:
		if args.invert is False:
			if seq.id in keys:
				print(seq.format("fasta"))
			if args.outfile is not None:
				SeqIO.write(seq, outFile, "fasta")
		else:
	# If the --invert/-i flag is given, print all fastas NOT listed in the keyfile
			if seq.id not in keys:
				print(seq.format("fasta"))
			if args.outfile is not None:
				SeqIO.write(seq, outFile, "fasta")

if __name__ == "__main__":
	main()

Hi,
I am trying to use this code on my multi-fasta file. Can you please elaborate on how exactly to use this script. What could be the input? and in what format. If possible can you provide an example? I am new in python usage
Thank you so much. appreciate it.

Hi Vasu,

This code is a little old, so try the newer version available here: https://github.com/jrjhealey/bioinfo-tools/blob/master/fastafetcher.py

If you run the code as python fastafetcher.py --help, it will tell you exactly what's needed to run it. You will need the biopython package installed for it to work.

Hi,
I did copy the code from https://github.com/jrjhealey/bioinfo-tools/blob/master/fastafetcher.py. I tried running it a suggested in the help file. there are many errors that pop up when I try and run it.
For example:
The command I used : python fastafetcher.py -f OG0000009.fa [-s "|OG0010404_batch_1|"] [-m {exact,partial}]
The error:
usage: fastafetcher.py [-h] -f FASTA [-k KEYFILE] [-s STRING] [-o OUTFILE] [-v] [-i] [-m {exact,partial}]
fastafetcher.py: error: unrecognized arguments: [-s |OG0010404_batch_1|] [-m exact] partial]

Here, OG0000009.fa is the fasta file to search in and "|OG0010404_batch_1|"] is my key word. I need to search in partial mode.
Please let me now if you can help me.

Thanks in advance,
Sanchita

You don't need to use the [ ] - these are convention to denote which arguments are optional.

You would simple run something like: fastafetcher.py -f /path/to/fasta.file -s "OG0010404_batch_1"

Depending on how the keys in your file are structured you may need the | characters you have, or you may need to use the -m partial or -m exact option too.

Hi again,
I realized that just after I wrote here. It works fine now.
Thank you.