apriltuesday/eva-common-pyutils

EBI EVA - Common Python Utilities

EBI EVA - Common Python Utilities

Assembly retrieval module

Create a object that will download and organise all the assemblies under onw directory. The scientific name is provided to place the assembly in a species specific subfolder. No checks are performed to see if the assembly and the species match.

from ebi_eva_common_pyutils.assembly import NCBIAssembly

assembly = NCBIAssembly('GCA_000008865.1', 'Escherichia coli O157:H7 str. Sakai', download_destination)
assembly.download_or_construct()
assembly.assembly_fasta_path

To only download the report

from ebi_eva_common_pyutils.assembly import NCBIAssembly

assembly = NCBIAssembly('GCA_000008865.1', 'Escherichia coli O157:H7 str. Sakai', download_destination)
assembly.download_assembly_report()
assembly.assembly_report_path

Logging

Central logging is provided by the logger module which takes care of propagating all handler to any newly created logger. You need to create at least one handler for the logging to happen.

from ebi_eva_common_pyutils.logger import logging_config as log_cfg 
log_cfg.add_stderr_handler()
logger = log_cfg.get_logger(__name__)
logger.info('Information')

Or from any class

from ebi_eva_common_pyutils.logger import logging_config as log_cfg 

class Foo(log_cfg.AppLogger):

    def bar(self):
        self.info('Information')

def main():
    log_cfg.add_stderr_handler()