# Path: bipy/toolbox/trim.py
#     ADAPTERS = yaml.load(in_handle)
# class TrimGalore(AbstractStage):
# class Cutadapt(AbstractStage):
#     def __init__(self, config):
#     def get_adapters(self, chemistry):
#     def _in2out(self, in_file):
#     def __call__(self, in_file):
#     def __init__(self, config):
#     def _detect_fastq_format(self, in_file):
#     def in2trimmed(self, in_file):
#     def _get_adapters(self, chemistry):
#     def _rc_adapters(self, adapters):
#     def _cut_file(self, in_file):
#     def _get_lf_file(self, in_file):
#     def _run_se(self, in_file):
#     def _run_pe(self, in_files):
#     def __call__(self, in_file):


import yaml
import unittest
import os
import filecmp
from bipy.toolbox import trim

STAGENAME = "trim_galore"


class TestTrimgalore(unittest.TestCase):

    def setUp(self):
        self.config_file = "test/trim_galore/test_trim_galore.yaml"
        with open(self.config_file) as in_handle:
            self.config = yaml.load(in_handle)

        self.input_file = self.config["input"]
        self.gtf = self.config["annotation"]["file"]
        self.stage_config = self.config["stage"][STAGENAME]
        self.options = self.stage_config["options"]
        self.correct = self.config["correct"]

    def test_trim_galore(self):

# Path: bipy/toolbox/trim.py
#     ADAPTERS = yaml.load(in_handle)
# class TrimGalore(AbstractStage):
# class Cutadapt(AbstractStage):
#     def __init__(self, config):
#     def get_adapters(self, chemistry):
#     def _in2out(self, in_file):
#     def __call__(self, in_file):
#     def __init__(self, config):
#     def _detect_fastq_format(self, in_file):
#     def in2trimmed(self, in_file):
#     def _get_adapters(self, chemistry):
#     def _rc_adapters(self, adapters):
#     def _cut_file(self, in_file):
#     def _get_lf_file(self, in_file):
#     def _run_se(self, in_file):
#     def _run_pe(self, in_files):
#     def __call__(self, in_file):


# Path: test/trim_galore/test_trim_galore.py
import yaml
import unittest
import os
import filecmp
from bipy.toolbox import trim


STAGENAME = "trim_galore"


class TestTrimgalore(unittest.TestCase):

    def setUp(self):
        self.config_file = "test/trim_galore/test_trim_galore.yaml"
        with open(self.config_file) as in_handle:
            self.config = yaml.load(in_handle)

        self.input_file = self.config["input"]
        self.gtf = self.config["annotation"]["file"]
        self.stage_config = self.config["stage"][STAGENAME]
        self.options = self.stage_config["options"]
        self.correct = self.config["correct"]

    def test_trim_galore(self):

        trim_galore = trim.TrimGalore(self.config)