Metadata-Version: 2.1
Name: Replidec
Version: 0.2.0
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
        ```
        
        ## Install
        ```
        pip3 install Replidec
        ```
        
        ## Usage
        ```
        Replidec [para]
        ```
        
        Replidec cantain 6 different program:  'multiSeqAsOne','batch','multiSeqEachAsOne','test_multiSeqAsOne','test_batch','test_multiSeqEachAsOne' 
        
        * multiSeqAsOne mode: input is a plain text file contain two coloumn (seprator must be **tab**)
        
           first column: sample name;
        
           second column: path of the protein file from one virues
        
        * multiSeqEachAsOne mode: input is a sequence file and treat each seqence as from one virus;
        
        * batch mode: input is a plain text file contain two coloumn (seprator must be **tab**);
        
           first column: sample name;
        
           second column: path of the protein file from one virues;
        
        * test_* mode: test for each prpgram
        
        ## Example
        ```
        ## test passed - test_multiSeqAsOne
        Replidec -p test_multiSeqAsOne
        
        ## test passsed - test_multiSeqEachAsOne
        Replidec -p test_multiSeqEachAsOne
        
        ## test passsed - test_batch
        Replidec -p test_batch
        
        ## test passed - multiSeqAsOne
        Replidec -p multiSeqAsOne -i example/genome_test.small.index -w multiSeqAsOne
        
        ## test passed - multiSeqEachAsOne
        Replidec -p multiSeqEachAsOne -i example/test.contig.small.fa -w multiSeqEachAsOne
        
        ## test passed - batch
        Replidec -p batch -i example/example.small.list -w batch
        ```
        
        
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
