#! /usr/bin/env python3

import sys
import os
import glob
import argparse

parser = argparse.ArgumentParser(description='Merge FASTA files')
parser.add_argument(
		'dir',
		type=str,
		help='directory with FASTA file'
	)
parser.add_argument(
		'--nondel',
		dest='nondel',
		action='store_true',
		help='Non-deleting propagation',
	)

args = parser.parse_args()

dir_fn=args.dir
if args.nondel:
	suffix="full.fa"
else:
	suffix="reduced.fa"

os.chdir(dir_fn)
fa_fns=glob.glob("*.{}".format(suffix))
fa_fns.sort()
for fn in fa_fns:
	print("Processing '{}'".format(fn), file=sys.stderr)

	node=fn.replace("."+suffix,"")

	with open(fn) as f:
		for x in f:
			if len(x)==0:
				continue
			if x[0]==">":
				print (">{}_{}".format(node,x[1:]),end="")
			else:
				print(x,end="")



#! /usr/bin/env python3

import sys
import os
import glob
import argparse

parser = argparse.ArgumentParser(description='Merge FASTA files')
parser.add_argument(
		'dir',
		type=str,
		help='directory with FASTA file'
	)
parser.add_argument(
		'--nondel',
		dest='nondel',
		action='store_true',
		help='Non-deleting propagation',
	)

args = parser.parse_args()

dir_fn=args.dir
if args.nondel:
	suffix="full.fa"
else:
	suffix="reduced.fa"

os.chdir(dir_fn)
fa_fns=glob.glob("*.{}".format(suffix))
fa_fns.sort()
for fn in fa_fns:
	print("Processing '{}'".format(fn), file=sys.stderr)

	node=fn.replace("."+suffix,"")

	with open(fn) as f:
		for x in f:
			if len(x)==0:
				continue
			if x[0]==">":
				print (">{}@{}".format(node,x[1:]),end="")
			else:
				print(x,end="")



Fix separator