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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# pauvre - just a pore plotting package
# Copyright (c) 2016-2018 Darrin T. Schultz. All rights reserved.
#
# This file is part of pauvre.
#
# pauvre is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# pauvre is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with pauvre. If not, see <http://www.gnu.org/licenses/>.
import os
import subprocess as sp
import unittest
class libSeq_test_case(unittest.TestCase):
"""Tests that different features of synplot work correctly
"""
def setUp(self):
# Here we must safely make the test directory if it does
# not exist
scriptdir = os.path.dirname(os.path.realpath(__file__))
testoutputdir = os.path.join(scriptdir, "testresults")
if not os.path.exists(testoutputdir):
os.makedirs(testoutputdir)
# now we see if the specific subdirectory for the program
# we are testing exists
self.thisoutdir = os.path.join(testoutputdir, "synplot")
if not os.path.exists(self.thisoutdir):
os.makedirs(self.thisoutdir)
# now we change our working directory to the
# specific subdirectory for this file
self.aln_dir = os.path.join(scriptdir, "testdata/alignments/")
self.gff1 = os.path.join(scriptdir, "testdata/gff_files/Bf201706.gff")
self.gff2 = os.path.join(scriptdir, "testdata/gff_files/JN392469.gff")
self.gff3 = os.path.join(scriptdir, "testdata/gff_files/NC016117.gff")
def test_normal_plotting_scenario(self):
"""This verifies that the LibSeq class is constructed with all of the
parameters that are present in the meraculous config files"""
os.chdir(self.thisoutdir)
thiscommand = """pauvre synplot --aln_dir {0} \
--fileform pdf \
--gff_paths {1} {2} {3} \
--center_on COX1 \
--gff_labels "B. forskalii" "P. bachei" "M. leidyi" """.format(
self.aln_dir, self.gff1,
self.gff2, self.gff3)
data = sp.Popen(thiscommand, shell = True,
stdout=sp.PIPE)
print("The data is:", data.communicate()[0].decode())
print("The return code is: ", data.returncode)
self.assertEqual(0, int(data.returncode))
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