Metadata-Version: 2.1
Name: orthofisher
Version: 0.0.4
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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            ·
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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 />
        
        ---
        
        <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/clipkit
        
        <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 291,604 sequence similarity searches across 1,294 eukaryotic proteomes, the performance of orthofisher was compared to results obtained from BUSCO. Examination of precision, recall, and F-measure revealed the efficacy of orthofisher's approach. More specifically, orthofisher had a <strong>recall of 1.0, precision of 0.978195, and an F-measure of 0.988977</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
