Metadata-Version: 2.1
Name: Replidec
Version: 0.2.1
Summary: Replication Cycle Detector for Phages
Home-page: https://github.com/pengSherryYel/Replidec_v0.2.1
Author: Xue Peng
Author-email: xue.peng@helmholtz-muenchen.de
License: UNKNOWN
Description: # Replidec: Replication Cycle Detector for Phages
        ## Aim
        
        Use bayes classifier combine with homology search to predict virus replication cycle
        
        ### Important: 
        
        mmseqs, hmmsearch, blastp must set to $PATH, these software can equal or higher than version list below
        
            MMseqs2 Version: 13.45111
        
            HMMER 3.3.2 (Nov 2020)
        
            Protein-Protein BLAST 2.5.0+
        
        ```
        conda create -n replidec
        conda activate replidec
        conda install -c bioconda,anaconda "python>=3.8" mmseqs2 hmmer blast
        ```
        ## Usage
        add the destination dir(where you clone the tool) in your path
        
        ```
        import sys
        sys.path.append("your_path/bayes_classifier")
        ```
        
        ## Example
        
        `from lifestyleBC import bayes_classifier_single,bayes_classifier_batch`
        
        for singe predict    
        
        `bayes_classifier_single("./example/simulate_art_sample1.5.faa","simulate_art_sample1.5","./test")`
        
        output --> list
        
        [prefix, inte_label, excision_label, pfam_label, p_total_temperate, p_total_lytic, bc_label, final_label]
        
        for batch predict
        
        `bayes_classifier_batch("./example/example.list","./batch_test","BC_predict.summary")`
        
        output --> file same column like above
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.8
Description-Content-Type: text/markdown
