# Path: ariba/ref_genes_getter.py
# class Error (Exception): pass
# class RefGenesGetter:
#     def __init__(self, ref_db, version=None, debug=False):
#     def _get_card_versions(self, tmp_file):
#     def _get_from_card(self, outprefix):
#     def _get_genetic_epi_database_from_bitbucket(cls, db_name, outdir, git_commit=None):
#     def _get_from_resfinder(self, outprefix):
#     def _get_from_argannot(self, outprefix):
#     def _get_from_megares(self, outprefix):
#     def _get_from_plasmidfinder(self, outprefix):
#     def _get_from_srst2_argannot(self, outprefix):
#     def _get_from_vfdb_core(self, outprefix):
#     def _get_from_vfdb_full(self, outprefix):
#     def _get_from_vfdb_common(self, outprefix, filename, info_text):
#     def _fix_virulencefinder_fasta_file(cls, infile, outfile):
#     def _get_from_virulencefinder(self, outprefix):
#     def _get_from_ncbi(self, outprefix, test=None): ## author github:schultzm
#     def run(self, outprefix):
#         BIOPROJECT = "PRJNA313047" ## https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA313047
#         RETMAX=100000000


import unittest
import os
import filecmp
from ariba import ref_genes_getter

modules_dir = os.path.dirname(os.path.abspath(ref_genes_getter.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')


class TestRefGenesGetter(unittest.TestCase):
    def test_fix_virulencefinder_fasta_file(self):
        '''test _fix_virulencefinder_fasta_file'''
        infile = os.path.join(data_dir, 'ref_genes_getter.fix_virulencefinder_fasta_file.in.fa')
        tmp_file = 'tmp.test.ref_genes_getter.fix_virulencefinder_fasta_file.out.fa'
        expected_file = os.path.join(data_dir, 'ref_genes_getter.fix_virulencefinder_fasta_file.out.fa')

# Path: ariba/ref_genes_getter.py
# class Error (Exception): pass
# class RefGenesGetter:
#     def __init__(self, ref_db, version=None, debug=False):
#     def _get_card_versions(self, tmp_file):
#     def _get_from_card(self, outprefix):
#     def _get_genetic_epi_database_from_bitbucket(cls, db_name, outdir, git_commit=None):
#     def _get_from_resfinder(self, outprefix):
#     def _get_from_argannot(self, outprefix):
#     def _get_from_megares(self, outprefix):
#     def _get_from_plasmidfinder(self, outprefix):
#     def _get_from_srst2_argannot(self, outprefix):
#     def _get_from_vfdb_core(self, outprefix):
#     def _get_from_vfdb_full(self, outprefix):
#     def _get_from_vfdb_common(self, outprefix, filename, info_text):
#     def _fix_virulencefinder_fasta_file(cls, infile, outfile):
#     def _get_from_virulencefinder(self, outprefix):
#     def _get_from_ncbi(self, outprefix, test=None): ## author github:schultzm
#     def run(self, outprefix):
#         BIOPROJECT = "PRJNA313047" ## https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA313047
#         RETMAX=100000000


# Path: ariba/tests/ref_genes_getter_test.py
import unittest
import os
import filecmp
from ariba import ref_genes_getter


modules_dir = os.path.dirname(os.path.abspath(ref_genes_getter.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')


class TestRefGenesGetter(unittest.TestCase):
    def test_fix_virulencefinder_fasta_file(self):
        '''test _fix_virulencefinder_fasta_file'''
        infile = os.path.join(data_dir, 'ref_genes_getter.fix_virulencefinder_fasta_file.in.fa')
        tmp_file = 'tmp.test.ref_genes_getter.fix_virulencefinder_fasta_file.out.fa'
        expected_file = os.path.join(data_dir, 'ref_genes_getter.fix_virulencefinder_fasta_file.out.fa')

        ref_genes_getter.RefGenesGetter._fix_virulencefinder_fasta_file(infile, tmp_file)