# Path: kleborate/__main__.py
# def get_rmp_mlst_results(data_folder, contigs, args):
#     return get_virulence_cluster_results(data_folder, contigs, 'rmp_alleles.fasta',
#                                          'RmST_profiles.txt', 'RmpADC', 'RmST',
#                                          'rmp unknown', 2, get_rmp_mlst_header, args)
# 
# def get_rmpa2_results(data_folder, contigs, args):
#     seqs = data_folder + '/rmpA2.fasta'
#     rmpa2_allele = rmpa2_blast(seqs, [contigs], args.min_coverage, args.min_identity)
#     return {'rmpA2': rmpa2_allele}


import collections
import unittest
from kleborate.__main__ import get_rmp_mlst_results, get_rmpa2_results
        self.assertEqual(results['rmpC'], '4-17%')
        self.assertEqual(results['RmpADC'], 'rmp 2A; VP (truncated)')
        self.assertEqual(results['RmST'], '21')

    def test_rmp_novel(self):
        """
        This test is an exact match for alleles, but an unknown combination.
        """
        results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_3.fasta', self.args)
        self.assertEqual(results['rmpA'], '8')
        self.assertEqual(results['rmpD'], '1')
        self.assertEqual(results['rmpC'], '9-11%')
        self.assertEqual(results['RmpADC'], 'rmp unknown')
        self.assertEqual(results['RmST'], '0')

    def test_rmp_missing_1(self):
        """
        This test is a match for RmST1, except that it's missing rmpC.
        """
        results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_4.fasta', self.args)
        self.assertEqual(results['rmpA'], '41-54%')
        self.assertEqual(results['rmpD'], '20')
        self.assertEqual(results['rmpC'], '-')
        self.assertEqual(results['RmpADC'], 'rmp 2A; VP (incomplete) (truncated)')
        self.assertEqual(results['RmST'], '1-1LV')

    def test_rmpa2_random(self):
        """
        This test has just random sequence and should give no rmpA2 call.
        """

# Path: kleborate/__main__.py
# def get_rmp_mlst_results(data_folder, contigs, args):
#     return get_virulence_cluster_results(data_folder, contigs, 'rmp_alleles.fasta',
#                                          'RmST_profiles.txt', 'RmpADC', 'RmST',
#                                          'rmp unknown', 2, get_rmp_mlst_header, args)
# 
# def get_rmpa2_results(data_folder, contigs, args):
#     seqs = data_folder + '/rmpA2.fasta'
#     rmpa2_allele = rmpa2_blast(seqs, [contigs], args.min_coverage, args.min_identity)
#     return {'rmpA2': rmpa2_allele}


# Path: test/test_rmp.py
import collections
import unittest
from kleborate.__main__ import get_rmp_mlst_results, get_rmpa2_results

        self.assertEqual(results['rmpC'], '4-17%')
        self.assertEqual(results['RmpADC'], 'rmp 2A; VP (truncated)')
        self.assertEqual(results['RmST'], '21')

    def test_rmp_novel(self):
        """
        This test is an exact match for alleles, but an unknown combination.
        """
        results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_3.fasta', self.args)
        self.assertEqual(results['rmpA'], '8')
        self.assertEqual(results['rmpD'], '1')
        self.assertEqual(results['rmpC'], '9-11%')
        self.assertEqual(results['RmpADC'], 'rmp unknown')
        self.assertEqual(results['RmST'], '0')

    def test_rmp_missing_1(self):
        """
        This test is a match for RmST1, except that it's missing rmpC.
        """
        results = get_rmp_mlst_results(self.data_dir, 'test/test_rmp/test_rmp_4.fasta', self.args)
        self.assertEqual(results['rmpA'], '41-54%')
        self.assertEqual(results['rmpD'], '20')
        self.assertEqual(results['rmpC'], '-')
        self.assertEqual(results['RmpADC'], 'rmp 2A; VP (incomplete) (truncated)')
        self.assertEqual(results['RmST'], '1-1LV')

    def test_rmpa2_random(self):
        """
        This test has just random sequence and should give no rmpA2 call.
        """

        results = get_rmpa2_results(self.data_dir, 'test/test_rmp/test_random.fasta', self.args)