# Path: circlator/minimus2.py
# class Error (Exception): pass
# class Merger:
#     def __init__(self,
#       assembly_fasta,
#       outprefix,
#       merge=True,
#     ):
#     def check_path(self, program):
#     def _write_split_contig(self, contig, outfile):
#     def _run_minimus2(self, infile, outdir):
#     def _run_minimus2_on_one_contig(self, contig):
#     def _run_minimus2_on_each_contig(self, infile, outfile):
#     def _run_initial_merge(self, infile, outdir):
#     def run(self):


import unittest
import filecmp
import os
import shutil
import pyfastaq
from circlator import minimus2

modules_dir = os.path.dirname(os.path.abspath(minimus2.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')

# It's likely that some people will not want to run the minimus2 pipeline at
# all, and just use the circlator pipeline. So we check if amos is installed
# and only run the tests if it is installed.
try:

# Path: circlator/minimus2.py
# class Error (Exception): pass
# class Merger:
#     def __init__(self,
#       assembly_fasta,
#       outprefix,
#       merge=True,
#     ):
#     def check_path(self, program):
#     def _write_split_contig(self, contig, outfile):
#     def _run_minimus2(self, infile, outdir):
#     def _run_minimus2_on_one_contig(self, contig):
#     def _run_minimus2_on_each_contig(self, infile, outfile):
#     def _run_initial_merge(self, infile, outdir):
#     def run(self):


# Path: circlator/tests/minimus2_test.py
import unittest
import filecmp
import os
import shutil
import pyfastaq
from circlator import minimus2


modules_dir = os.path.dirname(os.path.abspath(minimus2.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')

# It's likely that some people will not want to run the minimus2 pipeline at
# all, and just use the circlator pipeline. So we check if amos is installed
# and only run the tests if it is installed.
try:

    merger = minimus2.Merger(