import os
from pyfaidx import FastaIndexingError, BedError, FetchError
from pyfaidx.cli import main
from nose.tools import raises
from unittest import TestCase

path = os.path.dirname(__file__)
os.chdir(path)


class TestCLI(TestCase):
    def setUp(self):
        pass

    def tearDown(self):
        try:
            os.remove('data/genes.fasta.fai')
        except EnvironmentError:
            pass  # some tests may delete this file

    @raises(BedError)
    def test_short_line_lengths(self):
        main(['data/genes.fasta', '--bed', 'data/malformed.bed'])

    def test_fetch_whole_file(self):
        main(['data/genes.fasta'])

    def test_split_entry(self):
        main(['--split-files', 'data/genes.fasta', 'gi|557361099|gb|KF435150.1|'])
        assert os.path.exists('gi557361099gbKF435150.1.fasta')
        os.remove('gi557361099gbKF435150.1.fasta')

    @raises(FetchError)
    def test_fetch_error(self):
        main(['data/genes.fasta', 'gi|557361099|gb|KF435150.1|:1-1000'])
        
    def test_key_warning(self):
        main(['data/genes.fasta', 'foo'])