adtoolbox 0.1.0__py3-none-any.whl
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- adtoolbox/.DS_Store +0 -0
- adtoolbox/__init__.py +35 -0
- adtoolbox/__main__.py +7 -0
- adtoolbox/adm.py +2172 -0
- adtoolbox/bio_struct.py +73 -0
- adtoolbox/cli.py +496 -0
- adtoolbox/configs.py +331 -0
- adtoolbox/core.py +2158 -0
- adtoolbox/metagenomics_report.py +461 -0
- adtoolbox/optimize.py +524 -0
- adtoolbox/pipeline.py +47 -0
- adtoolbox/pkg_data/.DS_Store +0 -0
- adtoolbox/pkg_data/ADToolbox_Configs.json +1 -0
- adtoolbox/pkg_data/Modified_ADM_Map.json +1 -0
- adtoolbox/pkg_data/Modified_ADM_Model.json +808 -0
- adtoolbox/pkg_data/README.md +244 -0
- adtoolbox/pkg_data/qiime_template_paired.txt +32 -0
- adtoolbox/pkg_data/qiime_template_single.txt +34 -0
- adtoolbox/pkg_data/slurm_template.txt +12 -0
- adtoolbox/stats.py +82 -0
- adtoolbox/tables.py +221 -0
- adtoolbox/utils.py +408 -0
- adtoolbox-0.1.0.dist-info/METADATA +41 -0
- adtoolbox-0.1.0.dist-info/RECORD +26 -0
- adtoolbox-0.1.0.dist-info/WHEEL +4 -0
- adtoolbox-0.1.0.dist-info/entry_points.txt +3 -0
adtoolbox/.DS_Store
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Binary file
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adtoolbox/__init__.py
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import json
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import os
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import rich
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from rich.prompt import Prompt
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import sys
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"""Project Setup for ADToolBox."""
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__version__ = "1.0.0"
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sys.path.append(os.path.join(os.path.dirname(__file__)))
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PKG_DATA=os.path.join(os.path.dirname(os.path.realpath(__file__)),"pkg_data")
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with open(os.path.join(PKG_DATA,"ADToolbox_Configs.json"),"r") as f:
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conf = json.load(f)
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Main_Dir=conf["Base_Dir"]
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if Main_Dir and os.path.exists(Main_Dir):
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pass
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elif Main_Dir and not os.path.exists(Main_Dir):
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Main_Dir=input(f"Base directory is not configured properly.\nPlease input the correct path for the base directory:")
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if not os.path.exists(Main_Dir):
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os.makedirs(Main_Dir)
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rich.print(f"[green]Base directory is set to {Main_Dir}")
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else:
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Main_Dir=Prompt.ask("No Base Directory Found: \nWhere do you want to store your ADToolBox Data?")
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if not os.path.exists(Main_Dir):
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os.mkdir(Main_Dir)
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rich.print(f"\nDirectory did not exist. Created directory: {Main_Dir}")
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with open(os.path.join(os.path.dirname(os.path.realpath(__file__)),"pkg_data","ADToolbox_Configs.json"),"w") as f:
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conf["Base_Dir"]=Main_Dir
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json.dump(conf,f)
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