Metadata-Version: 2.1
Name: automlsa2
Version: 0.7.1
Summary: Automated Multi-Locus Sequence Analysis tool
Home-page: https://github.com/davised/automlsa2
Author: Edward Davis
Author-email: ed@cgrb.oregonstate.edu
Maintainer: Edward Davis
Maintainer-email: ed@cgrb.oregonstate.edu
License: Custom
Description: automlsa2
        =========
        
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        .. contents:: **Table of Contents**
            :backlinks: none
        
        Who might want this software?
        -----------------------------
        
        The intended audience is scientific researchers, computational biologists, and
        bioinformaticians who are interested in exploring phylogenetic and phylogenomic
        relationships between genes and organisms. The general idea is to allow the
        input of sequence data along with marker genes and output a robust phylogenetic
        tree. I've implemented commands to help with the installation of external
        dependencies, and I hope the software is easy to use.
        
        If you have feature requests or otherwise have ideas about how to make this
        software better, please submit an issue with your ideas!
        
        PhD/Masters students and undergraduates are especially encouraged to submit
        issues if they are having trouble using this software.
        
        Windows users, please install WSL to make use of this software. Using a Linux
        distribution will make your life as a computational researcher significantly
        easier.
        
        Installation
        ------------
        
        automlsa2 is distributed on `PyPI <https://pypi.org/project/automlsa2/>`_ as
        a universal wheel and is available on Linux/macOS and Windows (untested) and
        supports Python 3.7+ and PyPy.
        
        .. code-block:: bash
        
            $ python3 -m pip install -U automlsa2
        
        While I will do my best to keep the git version usable, stick to a release
        and/or pypi install for the most stable experience.
        
        git version install:
        
        .. code-block:: bash
        
            $ git clone https://github.com/davised/automlsa2.git
            $ cd automlsa2
            $ python3 -m pip install -r requirements.txt
            $ python3 -m pip install -U .
        
        for developers, clone as above, then:
        
        .. code-block:: bash
        
            $ python3 -m pip install -e . --no-use-pep517
        
        Dependencies
        ------------
        
        Python modules:
        
        1. pandas
        2. numpy
        3. biopython
        4. rich
        5. packaging
        
        See ``requirements.txt`` for more info.
        
        External programs:
        
        1. `NCBI BLAST+ >= 2.10.0 <https://blast.ncbi.nlm.nih.gov>`_
        2. `mafft >= 7.471 <https://mafft.cbrc.jp/alignment/software/>`_
        3. `IQ-TREE COVID-19 release >= 2.1.1 <http://www.iqtree.org>`_
        
        You can install external programs using the ``automlsa2 --install_deps``
        command. These will be installed to ``${HOME}/.local/external`` unless
        otherwise specified.
        
        Just tell me how to run it
        --------------------------
        
        .. code-block:: bash
        
            $ automlsa2 --files Genus_species_1.fna Genus_species_2.fna ... \
              Genus_species_N.fna --query queries.fasta -t THREADS -- runID
        
        Alternatively:
        
        .. code-block:: bash
        
            $ automlsa2 --dir path/to/genomes --query queries.fasta -t THREADS \
              -- runID
        
        
        Overview
        --------
        
        automlsa2 is a re-imagination of `autoMLSA.pl
        <https://github.com/osuchanglab/autoMLSA>`_
        
        The entire codebase has been re-written in python. While the general algorithm
        produces similar output, and several steps are shared, there are many
        updates and differences between the two programs, which will be covered later.
        
        The general overview can be summarized here:
        
        0. Input is a set of marker genes as queries, and a set of target genome FASTA
           files.
        1. BLAST databases are generated for each target genome, and each query gene
           is extracted from the input query FASTA files.
        2. BLAST searches are done with the extracted sequences and genomes.
        3. Per genome hits are calculated pending the cut-offs, and genomes are
           filtered from the analysis.
        4. Sequences are extracted from the BLAST results as unaligned multi-FASTAs.
        5. Unaligned sequences are aligned using mafft.
        6. A nexus file is generated pointing to all aligned sequences.
        7. A phylogenetic tree is generated using the nexus file as input.
        
        BLAST searches are threaded, or, optionally, written to a file to be submitted
        to a compute cluster. mafft alignment commands can also be written to a file
        for submission to a compute cluster.
        
        Input query files and genome directories are scanned for updates - if
        sequences are added, removed, or changed, the analysis is re-done.
        
        Multiple queries targeting the same gene sequence can be used to improve
        coverage of disparate gene sequences, e.g. attempting to cover an entire
        phylum with multiple reference genomes being used.
        
        Usage
        -----
        
        .. code-block:: bash
        
            $ automlsa2 -h
            usage: automlsa2 [-h] [--query QUERY [QUERY ...]] [--files FILES [FILES ...]]
                         [--dir DIR [DIR ...]] [-e EVALUE] [-c COVERAGE] [-i IDENTITY]
                         [-p {blastn,tblastn}] [--config CONFIG] [--missing_check]
                         [-t THREADS] [--dups] [--allow_missing ALLOW_MISSING]
                         [--outgroup OUTGROUP] [--protect]
                         [--checkpoint {validate,preblast,filtering,prealign,postalign,nexus,none}]
                         [--install_deps [INSTALL_DEPS]] [--external EXTERNAL]
                         [--mafft MAFFT] [--iqtree IQTREE] [--debug] [--version]
                         [--quiet]
                         runid
        
            This is a rewrite of autoMLSA.pl. Generates automated multi-locus sequence analyses.
        
            positional arguments:
              runid                 Name of the run directory.
        
        optional arguments:
        
        -h, --help                        show this help message and exit
        --query <QUERY [QUERY ...]>       Path to file with input seq(s).
        --files <FILES [FILES ...]>       Path to the target genome FASTA files.
        --dir <DIR [DIR ...]>             Path to the target genome directory with FASTA files.
        -e EVALUE, --evalue EVALUE        E-value cutoff for BLAST searches. [1e-5]
        -c COVERAGE, --coverage COVERAGE  Sets the coverage cut-off threshold. [50]
        -i IDENTITY, --identity IDENTITY  Sets the identity cut-off threshold. [30]
        -p PROGRAM, --program PROGRAM     Which BLAST program to run. [tblastn] {tblastn, blastn}
        --config CONFIG                   Path to configuration json file to copy.
        --missing_check                   Use this to confirm that settings have been
                                          checked when genes are missing.
        -t THREADS, --threads THREADS     Number of threads to use. [1]
        --dups                            Allow for duplicate query names for more sequence
                                          coverage across disparate organisms.
        --allow_missing ALLOW_MISSING     Allow for N missing genes per genome. [0]
        --outgroup OUTGROUP               Name of outgroup file or strain to root on.
        --protect                         Save files from getting overwritten. By default, as input
                                          files update, older alignments and trees are deleted.
        --checkpoint CHECKPOINT           Name of stage to stop computing on. [none]
                                          {validate,preblast,filtering,prealign,postalign,nexus,none}
        --install_deps <[INSTALL_DEPS]>   Install dependencies into given directory. [~/.local/external]
        --external EXTERNAL               Path to installed external programs. [~/.local/external]
        --mafft MAFFT                     mafft settings [--localpair --maxiterate 1000 --reorder]
        --iqtree IQTREE                   iqtree2 settings [-m MFP -B 1000 -alrt 1000 --msub
                                          nuclear --merge rclusterf]
        --debug                           Turn on debugging messages.
        --version                         show program's version number and exit
        --quiet                           Turn off progress messages.
        
        One or more input target genome FASTA files is required, either using
        ``--files`` or ``--dir``. Additionally, one or more query FASTA files
        containing one or more query gene sequences is necessary for analysis.
        
        By default, protein queries are expected, and nucleotide FASTA sequence is
        required for the target genomes. ``tblastn`` is used to target the genome
        sequences using the amino acid queries. ``blastn`` is also available, targeting
        the genome sequences using nucleotide queries.
        
        Threads will speed things up significantly. BLAST searches are threaded in
        python; submitting multiple threads to the blast executable often does not
        result in much speed up, so each BLAST search is run with one CPU given.
        
        Query marker genes often come from a well-studied representative of, at most,
        the same genus. Intergenera phylogenies should have a representative sequence
        from each genus. This can be accomplished by giving all examples of a
        particular gene the same name in the reference FASTA file. e.g.
        
        .. code-block:: bash
        
          >Gene1 Refgenus1 refspecies ABC
          <AA sequence>
          >Gene1 Refgenus2 refspecies DEF
          <AA sequence>
          >Gene1 Refgenus3 refspecies GHI
          <AA sequence>
        
        This ^ FASTA ^ file would have three representatives of Gene1 in the analysis.
        The resulting alignments would have one copy of the gene, with the best hits
        from each target genome included.
        
        Target genome files will be named based on the filename in the final output.
        Generally, one will want to have Genus_species_strain.fasta or
        G_species_strain.fasta as the filenames prior to analysis.
        
        Genomes can be downloaded using my ``get_assemblies`` program, here:
        https://pypi.org/project/get-assemblies/. Locally produced genomes can be
        renamed as required.
        
        TODO
        ----
        
        ☐ Write detailed list of intermediate files.
        
        ☐ Compare functionality of this version to prior autoMLSA.pl version.
        
        ☑ Check for version numbers for external programs.
        
        Contributing
        ------------
        
        Bug reports are encouraged! Submit a github issue and I'll be happy to take
        a look. Also, feel free to clone and submit merge requests.
        
        Author Contact
        --------------
        
        `Ed Davis <mailto:ed@cgrb.oregonstate.edu>`_
        
        Acknowledgments
        ----------------
        
        Special thanks for helping me test the software and get the python code packaged:
        
        * `Alex Weisberg <https://github.com/alexweisberg>`_
        * `Shawn O'Neil <https://github.com/oneilsh>`_
        
        Also, thanks to these groups for supporting me through my scientific career:
        
        * `OSU Chang Lab <https://github.com/osuchanglab>`_
        * `Center for Genome Research and Biocomputing @ OSU <https://cgrb.oregonstate.edu>`_
        
        License
        -------
        
        automlsa2 is distributed under the terms listed in the ``LICENSE`` file. The
        software is free for non-commercial use.
        
        Copyrights
        ----------
        
        Copyright (c) 2020 Oregon State University
        
        All Rights Reserved.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: Free for non-commercial use
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
