Metadata-Version: 1.0
Name: riptide
Version: 1.4
Summary: Reaction Inclusion by Parsimony and Transcript Distribution (RIPTiDe)
Home-page: https://github.com/mjenior/riptide
Author: Matt Jenior
Author-email: mattjenior@gmail.com
License: MIT
Description: RIPTiDe
        =======
        Reaction Inclusion by Parsimonious usage and Transcript Distribution
        
        
        ### Please cite when using:
        Jenior ML, Moutinho TJ, and Papin JA. (2019). Parsimonious transcript data integration improves context-specific predictions of bacterial metabolism in complex environments. BioRxiv. DOI 
        
        ### Dependencies
        cobrapy (>=version 0.13)
        
        symengine
        
        ### Installation:
        pip install riptide
        
        ### Example usage:
        from riptide import *
        
        my_model = cobra.io.read_sbml_model('examples/genre.sbml')
        
        transcript_abundances_1 = read_transcription_file('examples/transcriptome1.tsv')
        
        transcript_abundances_2 = read_transcription_file('examples/transcriptome2.tsv')
        
        contextualized_model_1, flux_samples_1 = riptide(my_model, transcript_abundances_1)
        
        contextualized_model_2, flux_samples_2 = riptide(my_model, transcript_abundances_2)
        
        
            read_transcription_file() parameters
            ----------
            read_abundances_file : string
                User-provided file name which contains gene IDs and associated transcription values
            header : boolean
                Defines if read abundance file has a header that needs to be ignored
                default is no header
            replicates : boolean
                Defines if read abundances contains replicates and medians require calculation
                default is no replicates
            sep: string
                Defines what character separates entries on each line
                defaults to tab (.tsv)
        
        
            riptide() parameters
            ----------
            model : cobra.Model
                The model to be contextualized
            transcription : dictionary
                Dictionary of transcript abundances, output of read_transcription_file()
            defined : False or File
                Text file containing reactions IDs for forced inclusion listed on the first line and exclusion 
                listed on the second line (both .csv and .tsv formats supported)
            sampling : int or False
                Number of flux samples to collect, default is 10000, If False, sampling skipped
            percentiles : list of floats
                Percentile cutoffs of transcript abundance for linear coefficient assignments to associated reactions
                Defaults are [50.0, 62.5, 75.0, 87.5]
            coefficients : list of floats
                Linear coefficients to weight reactions based on distribution placement
                Defaults are [1.0, 0.5, 0.1, 0.01, 0.001]
            fraction : float
                Minimum percent of optimal objective value during FBA steps
                Default is 0.8
            conservative : str
            	Conservatively remove inactive reactions based on GPR rules
            	Either 'y' or 'n', default in 'n' (no)
        
        
Platform: UNKNOWN
