utils_io.py

# shared variables and functions

import os, json
from Bio import SeqIO

def read_json(file_name):
	try:
		handle = open(file_name, 'r')
	except IOError:
		pass
	else:
		data = json.load(handle)
		handle.close()
	return data

def write_json(data, file_name, indent=1):
	try:
		handle = open(file_name, 'w')
	except IOError:
		pass
	else:
		json.dump(data, handle, indent=indent)
		handle.write("\n")
		handle.close()

def read_fasta(file_name):
	alignment = []
	try:
		handle = open(file_name, 'r')
	except IOError:
		pass
	else:
		for record in SeqIO.parse(handle, "fasta"):
			v = {
				"strain": record.description,
				"seq": str(record.seq).upper()
			}
			alignment.append(v)
		handle.close()
	return alignment

def write_fasta(viruses, file_name):
	try:
		handle = open(file_name, 'w')
	except IOError:
		pass
	else:
		for v in viruses:
			handle.write(">" + v['strain'] + "\n")
			handle.write(v['seq'] + "\n")
		handle.close()