diff --git a/geofetch/__init__.py b/geofetch/__init__.py index e1b75f9..3be93ae 100644 --- a/geofetch/__init__.py +++ b/geofetch/__init__.py @@ -1,18 +1,8 @@ """Package-level data""" -import coloredlogs -import logmuse - from geofetch._version import __version__ from geofetch.finder import Finder from geofetch.geofetch import Geofetcher __author__ = ["Oleksandr Khoroshevskyi", "Vince Reuter", "Nathan Sheffield"] __all__ = ["Finder", "Geofetcher", "__version__"] - -_LOGGER = logmuse.init_logger("geofetch") -coloredlogs.install( - logger=_LOGGER, - datefmt="%H:%M:%S", - fmt="[%(levelname)s] [%(asctime)s] %(message)s", -) diff --git a/geofetch/finder.py b/geofetch/finder.py index 587e1ae..084c922 100644 --- a/geofetch/finder.py +++ b/geofetch/finder.py @@ -3,7 +3,6 @@ import re from datetime import datetime, timedelta -import coloredlogs import requests import xmltodict @@ -19,11 +18,6 @@ __author__ = "Oleksandr Khoroshevskyi" _LOGGER = logging.getLogger("__name__") -coloredlogs.install( - logger=_LOGGER, - datefmt="%H:%M:%S", - fmt="[%(levelname)s] [%(asctime)s] %(message)s", -) class Finder: diff --git a/geofetch/geofetch.py b/geofetch/geofetch.py index 234d375..ed79b41 100755 --- a/geofetch/geofetch.py +++ b/geofetch/geofetch.py @@ -117,18 +117,18 @@ def __init__( :param input: GSEnumber or path to the input file :param name: Specify a project name. Defaults to GSE number or name of accessions file name :param metadata_root: Specify a parent folder location to store metadata. - The project name will be added as a subfolder [Default: $SRAMETA:] + The project name will be added as a subfolder (Default: $SRAMETA:) :param metadata_folder: Specify an absolute folder location to store metadata. No subfolder will be added. - Overrides value of --metadata-root [Default: Not used (--metadata-root is used by default)] + Overrides value of --metadata-root (Default: Not used, --metadata-root is used by default) :param just_metadata: If set, don't actually run downloads, just create metadata :param refresh_metadata: If set, re-download metadata even if it exists. :param config_template: Project config yaml file template. :param pipeline_samples: Specify one or more filepaths to SAMPLES pipeline interface yaml files. These will be added to the project config file to make it immediately compatible with looper. - [Default: null] + (Default: null) :param pipeline_project: Specify one or more filepaths to PROJECT pipeline interface yaml files. These will be added to the project config file to make it immediately compatible with looper. - [Default: null] + (Default: null) :param acc_anno: Produce annotation sheets for each accession. Project combined PEP for the whole project won't be produced. :param discard_soft: Create project without downloading soft files on the disc @@ -136,44 +136,44 @@ def __init__( :param disable_progressbar: Set true to disable progressbar :param const_limit_project: Optional: Limit of the number of the constant sample characters - that should not be in project yaml. [Default: 50] + that should not be in project yaml. (Default: 50) :param const_limit_discard: Optional: Limit of the number of the constant sample characters - that should not be discarded [Default: 250] + that should not be discarded (Default: 250) :param attr_limit_truncate: Optional: Limit of the number of sample characters. Any attribute with more than X characters will truncate to the first X, where X is a number of characters - [Default: 500] + (Default: 500) :param max_soft_size: Optional: Max size of soft file. - Supported input formats : 12B, 12KB, 12MB, 12GB. [Default value: 1GB] + Supported input formats : 12B, 12KB, 12MB, 12GB. (Default: 1GB) - :param processed: Download processed da_soft_sizeta [Default: download raw data]. + :param processed: Download processed data (Default: download raw data). :param data_source: Specifies the source of data on the GEO record to retrieve processed data, which may be attached to the collective series entity, or to individual samples. Allowable values are: - samples, series or both (all). Ignored unless 'processed' flag is set. [Default: samples] - :param filter: Filter regex for processed filenames [Default: None].Ignored unless 'processed' flag is set. - :param filter_size: Filter size for processed files that are stored as sample repository [Default: None]. + samples, series or both (all). Ignored unless 'processed' flag is set. (Default: samples) + :param filter: Filter regex for processed filenames (Default: None). Ignored unless 'processed' flag is set. + :param filter_size: Filter size for processed files that are stored as sample repository (Default: None). Works only for sample data. Supported input formats : 12B, 12KB, 12MB, 12GB. Ignored unless 'processed' flag is set. :param geo_folder: Specify a location to store processed GEO files. - Ignored unless 'processed' flag is set.[Default: $GEODATA:] + Ignored unless 'processed' flag is set. (Default: $GEODATA:) :param split_experiments: Split SRR runs into individual samples. By default, SRX experiments with multiple SRR Runs will have a single entry in the annotation table, with each run as a separate row in the - subannotation table. This setting instead treats each run as a separate sample [Works with raw data] + subannotation table. This setting instead treats each run as a separate sample (Works with raw data) :param bam_folder: Optional: Specify folder of bam files. Geofetch will not download sra files when - corresponding bam files already exist. [Default: $SRABAM:] [Works with raw data] + corresponding bam files already exist. (Default: $SRABAM:) (Works with raw data) :param fq_folder: Optional: Specify folder of fastq files. Geofetch will not download sra files when corresponding - fastq files already exist. [Default: $SRAFQ:] [Works with raw data] - :param use_key_subset: Use just the keys defined in this module when writing out metadata. [Works with raw data] + fastq files already exist. (Default: $SRAFQ:) (Works with raw data) + :param use_key_subset: Use just the keys defined in this module when writing out metadata. (Works with raw data) :param sra_folder: Optional: Specify a location to store sra files - [Default: $SRARAW:" + safe_echo("SRARAW") + ] - :param bam_conversion: Optional: set True to convert bam files [Works with raw data] + (Default: $SRARAW:" + safe_echo("SRARAW") + ) + :param bam_conversion: Optional: set True to convert bam files (Works with raw data) :param picard_path: Specify a path to the picard jar, if you want to convert fastq to bam - [Default: $PICARD:" + safe_echo("PICARD") + "] [Works with raw data] + (Default: $PICARD:" + safe_echo("PICARD") + ") (Works with raw data) :param add_convert_modifier: Add looper SRA convert modifier to config file. - :param skip: Skip some accessions. [Default: no skip]. - :param opts: opts object [Optional] + :param skip: Skip some accessions. (Default: no skip). + :param opts: opts object (Optional) :param str | int max_prefetch_size: argmuent to prefetch command's --max-size option; for reference: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump#check-the-maximum-size-limit-of-the-prefetch-tool :param kwargs: other values diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt index 9440999..883dc5e 100644 --- a/requirements/requirements-all.txt +++ b/requirements/requirements-all.txt @@ -1,10 +1,9 @@ colorama>=0.3.9 -logmuse>=0.2.6 +logmuse>=0.3.0 ubiquerg>=0.6.2 requests>=2.28.1 xmltodict>=0.13.0 pandas>=1.5.3 peppy>=0.40.6 rich>=12.5.1 -coloredlogs>=15.0.1 piper>=0.14.4