import os
import sys
import configparser
from subprocess import call

# project import
from . import logger
from .mapper import hisat2


def main(config_path):
    """ Main function of pro'gramme read configuration and run enable step """
    config = configparser.ConfigParser()

    logger.setup_logging(**config)

    config.read(config_path)
    print(config.sections())

    for key in config['paths']: print(config['paths'][key])


def trimming(files_dir, rep_out , paired=1) :
    file_list = os.listdir(files_dir)
    for fastq in file_list :
        call(['cmd', 'options...'])


if __name__ == "__main__":
    main(sys.argv[1])

import os
import sys
import configparser
from subprocess import call

# project import
from . import logger
from .mapper import hisat2


def main(config_path):
    """ Main function of pro'gramme read configuration and run enable step """
    config = configparser.ConfigParser()

    config.read(config_path)
    print(config.sections())
    logger.setup_logging(**config)

    for key in config['paths']: print(config['paths'][key])

    mapper = hisat2.Hisat2()
    mapper.read_configuration(**config)
    if mapper.check_configuration() :
        mapper.run()

def trimming(files_dir, rep_out , paired=1) :
    file_list = os.listdir(files_dir)
    for fastq in file_list :
        call(['cmd', 'options...'])


if __name__ == "__main__":
    main(sys.argv[1])

Add test of hisat2 object
Add test of hisat2 object

  import os
  import sys
  import configparser
  from subprocess import call
  
  # project import
  from . import logger
  from .mapper import hisat2
  
  
  def main(config_path):
      """ Main function of pro'gramme read configuration and run enable step """
      config = configparser.ConfigParser()
  
-     logger.setup_logging(**config)
- 
      config.read(config_path)
      print(config.sections())
+     logger.setup_logging(**config)
  
      for key in config['paths']: print(config['paths'][key])
  
+     mapper = hisat2.Hisat2()
+     mapper.read_configuration(**config)
+     if mapper.check_configuration() :
+         mapper.run()
  
  def trimming(files_dir, rep_out , paired=1) :
      file_list = os.listdir(files_dir)
      for fastq in file_list :
          call(['cmd', 'options...'])
  
  
  if __name__ == "__main__":
      main(sys.argv[1])
  
Add test of hisat2 object
## Code Before:
import os
import sys
import configparser
from subprocess import call

# project import
from . import logger
from .mapper import hisat2


def main(config_path):
    """ Main function of pro'gramme read configuration and run enable step """
    config = configparser.ConfigParser()

    logger.setup_logging(**config)

    config.read(config_path)
    print(config.sections())

    for key in config['paths']: print(config['paths'][key])


def trimming(files_dir, rep_out , paired=1) :
    file_list = os.listdir(files_dir)
    for fastq in file_list :
        call(['cmd', 'options...'])


if __name__ == "__main__":
    main(sys.argv[1])

## Instruction:
Add test of hisat2 object
## Code After:
import os
import sys
import configparser
from subprocess import call

# project import
from . import logger
from .mapper import hisat2


def main(config_path):
    """ Main function of pro'gramme read configuration and run enable step """
    config = configparser.ConfigParser()

    config.read(config_path)
    print(config.sections())
    logger.setup_logging(**config)

    for key in config['paths']: print(config['paths'][key])

    mapper = hisat2.Hisat2()
    mapper.read_configuration(**config)
    if mapper.check_configuration() :
        mapper.run()

def trimming(files_dir, rep_out , paired=1) :
    file_list = os.listdir(files_dir)
    for fastq in file_list :
        call(['cmd', 'options...'])


if __name__ == "__main__":
    main(sys.argv[1])
