Metadata-Version: 1.1
Name: curatedmetagenomicdata3
Version: 0.1.1
Summary: Python wrapper for curatedMetagenomicData3.
Home-page: https://github.com/kellylab/curatedmetagenomidata3-python
Author: UNKNOWN
Author-email: skhan8@mail.einstein.yu.edu
License: UNKNOWN
Description: # curatedMetagenomicData3-python
        
        Python Wrapper for curatedMetagenomicData3
        
        # Installation
        
            pip install curatedmetagenomicdata3
        
        # Usage
        
        ## Pre-requisites
        
            # Decide on a folder to store files in
            # This package downloads files containing raw annotation data based on your queries
        
            import curatedmetagenomicdata3 as cmd3
            source_dir = "test"
        
        ## 1) Open Metadata
        
            # This function returns a DataFrame containing all sample metadata
            df = cmd3.get_metadata()
        
        ## 2) Decide What Samples You Want Annotations for
        
            # For example, let's say you want to download taxonomic relative 
            # abundances data for all samples for Type 2 Diabetes patients
        
            t2d = df[df['disease'] == 'T2D']
        
        ## 3) Compile OTU Data for Chosen Samples
        
            # Taxonomic Relative Abundances
            taxa = assemble_taxa_dataset(t2d, source_dir)
        
        That's it! `taxa` will be a dataframe containing the relative abundances data for the samples you chose. All of the data for that will be downloaded and cached to `source_dir` automatically for future use.
        
        You can also get pathway abundances as well
        
            # Pathway Relative Abundances
            pathways = assemble_pathways_dataset(t2d, source_dir)
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
