Metadata-Version: 2.1
Name: orthofisher
Version: 0.1.2
Summary: orthofisher
Home-page: https://github.com/JLSteenwyk/orthofisher.git
Author: Jacob L. Steenwyk
Author-email: jlsteenwyk@gmail.com
License: UNKNOWN
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            ·
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        <br />
        
        Orthofisher conducts automated and high-throughout identification of a predetermined set of orthologs, which can be used for phylgenomics, gene family copy number determination and more!
        
        ---
        
        <br />
        
        ## Guide
        [Quick Start](#quick-start)<br />
        [Performance Assessment](#performance-assessment)<br />
        [FAQ](#faq)
        
        <br />
        
        ---
        
        <br/>
        
        ## Quick Start
        
        For detailed instructions on usage and a tutorial, please see the [online documentation](https://jlsteenwyk.com/orthofisher/).
        
        <br/>
        
        ### 1) Prerequisite
        Before installing orthofisher, please first install [HMMER3](http://hmmer.org/documentation.html) and add the HMMER to your .bashrc path. For example, my .bashrc has the following:
        
        ```shell
        export PATH=$PATH:/home/steenwj/SOFTWARE/hmmer-3.1b2-linux-intel-x86_64/binaries
        ```
        
        <br/>
        
        ### 2) Install orthofisher
        
        **If you are having trouble installing orthofisher, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**
        
        <br/>
        
        To install via *anaconda*, execute the follwoing command:
        ``` shell
        conda install -c jlsteenwyk orthofisher
        ```
        Visit here for more information: https://anaconda.org/jlsteenwyk/orthofisher
        
        <br/>
        
        To install via *pip*, execute the follwoing command:
        ```shell
        pip install orthofisher
        ```
        
        <br />
        
        To install from source, execute the follwoing command:
        ```shell
        # download
        git clone https://github.com/JLSteenwyk/orthofisher.git
        # change dir
        cd orthofisher/
        # install
        make install
        ```
        
        <br/>
        
        If you run into software dependency issues, install orthofisher in a virtual environment. To do so, create your virtual environment with the following command: 
        ```shell
        # create virtual environment
        python -m venv .venv
        # activate virtual environment
        source .venv/bin/activate
        ```
        
        Next, install the software using your preferred method above. Thereafter, you will be able to use orthofisher.
        
        To deactivate your virtual environment, use the following command:
        ```shell
        # deactivate virtual environment
        deactivate
        ```
        **Note, the virtual environment must be activated to use *orthofisher*.**
        
        <br />
        
        ---
        
        <br />
        
        ## Performance Assessment
        Using 1,530 sequence similarity searches across six model eukaryotic proteomes, the performance of orthofisher was compared to results obtained from BUSCO. Examination of precision and recall revealed near perfect performance. More specifically, orthofisher had a <strong>recall of 1.0 and precision of 0.99</strong>. Precision is less than 1.0 because priors of expected sequence length and sequence similarity scores--which are not implemented in orthofisher--resulted in more missing genes in the BUSCO pipeline than the orthofisher pipeline.
        
        <br />
        
        ---
        
        <br />
        
        ## FAQ
        
        <br />
        
        <strong>I am having trouble installing orthofisher, what should I do?</strong>
        
        Please install orthofisher using a virtual environment as described in the installation instructions. If you are still running into issues after installing in a virtual environment, please contact Jacob L. Steenwyk via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk).
        
        <br />
        
        ---
        
        <br />
        
        ### orthofisher is developed and maintained by [Jacob Steenwyk](https://jlsteenwyk.github.io/)
        
        
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
