Metadata-Version: 2.1
Name: metavariant
Version: 0.1.2
Summary: a lexical manipulation toolkit for genetic variant descriptors (hgvs, etc)
Home-page: UNKNOWN
Author: Naomi Most
Author-email: naomi@nthmost.com
Maintainer: Naomi Most
Maintainer-email: naomi@nthmost.com
License: Apache 2.0
Description: ******************************************************
        MetaVariant
        ******************************************************
        
        Python toolkit for parsing HGVS strings describing genetic variants (mutations)
        into components and generating lexical synonyms of these descriptors.
        
        Requirements
        ============
        
        You'll need a UNIX-like environment to use this package. Both OS X and Linux have been confirmed to work.
        
        Additionally, your system must contain the C development version of the client library
        for Postgres 9.3 or later (needed to connect to UTA services). 
        
        On OS X using brew:
        
        .. code-block:: bash
        
          $ brew install postgresql
        
        On Linux using Ubuntu:
        
        .. code-block:: bash
        
          $ apt-get install libpq-dev
        
        Python library dependencies for variant_lexicon are the following::
        
          numpy
          biopython
          uta
          hgvs
        
        The above "should" be successfully installed by using setup.py and/or by installing
        this package via pip.
        
        
        Optional but Recommended: IPython
        ---------------------------------
        
        Install ipython via pypi:
        
        .. code-block:: bash
        
          $ pip install ipython
          
        More installation options and instructions are available on `the iPython installation page <http://ipython.org/ipython-doc/stable/install/install.html>`_.
        
        Variant: shortcut to SequenceVariant
        ====================================
        
        `Variant` is an API shortcut to instantiating a SequenceVariant object from an HGVS string. It accepts
        both gene-name-bearing and non-gene-name-bearing HGVS strings. 
        
        See [Human Genome Variation Society](http://www.hgvs.org/) for explanation of HGVS strings.
        
        Examples of valid HGVS strings::
        
          NM_198056.2:c.4786T>A
          NC_000023.10:g.32841489delT
          NP_009225.1:p.Glu1000_Glu1001del
          NM_001165963.1(SCN1A):c.384_1662dup
          
        
        Note: some valid HGVS strings currently cannot be parsed by the hgvs library (as of 6/17/2016). Examples::
        
          NC_000001.11:g.(?_215888426)_(215900905_?)del
          NM_000251.2:c.212-?_366+?dup
        
        When an illogical or invalid HGVS string is provided to `Variant`, this function returns None. (Tune into 
        the "metavariant" logger at INFO level for information.)
        
        `Variant` will also accept a SequenceVariant object as its argument, returning the same variant (identity).
        
        
        VariantLVG: Lexical Variant Generation
        ======================================
        
        `VariantLVG` takes an hgvs.SequenceVariant object or a plain HGVS string and uses the Universal Transcript
        Archive (UTA) to find as many related transcripts and sequence variants as possible that could be used as
        "synonyms" of the provided variant.
        
        This class raises `CriticalHgvsError` upon instantiation if the supplied HGVS string fails to create a 
        valid SequenceVariant object.
        
        Usage example:
        
        .. code-block:: python
        
          hgvs_text = 'NM_198056.2:c.4786T>A'
          lex = VariantLVG(hgvs_text)
        
          print(lex.variants)
          print(lex.transcripts)
          print(lex.gene_name)
        
        Enrichment
        ----------
        
        VariantLVG provides for "enrichment" of lexical variant generation by allowing
        more transcripts and variations to be supplied at instantiation. Just use the 
        appropriate keyword for the type of information, remembering that the "enrichment"
        keyword arguments are all lists.
        
        Keyword Arguments
        -----------------
        
        - transcripts (list): list of strings describing valid alternative transcripts for seqvar
        - seqvar_max_len (int): restrict posedit lengths to this number of characters (or fewer).  
        - hgvs_c (list): see Enrichment above
        - hgvs_g (list): see Enrichment above
        - hgvs_n (list): see Enrichment above
        - hgvs_p (list): see Enrichment above
        
        Attributes
        ----------
        
        - hgvs_text: original hgvs string from instantiation
        - seqvar: original SequenceVariant from instantiation
        - transcripts: list of strings indicating related transcripts
        - variants: 2-level dictionary of shape { seqtype: { hgvs_text: seqvar } }
        
        Properties
        ----------
        
        + gene_name: returns HUGO gene-name if it can be ascertained using UTA. (Lazy-loaded attribute _gene_name.)
        + hgvs_c: returns flat list of c.DNA hgvs strings from variants
        + hgvs_g: returns flat list of g.DNA hgvs strings from variants
        + hgvs_n: returns flat list of n.RNA hgvs strings from variants 
        + hgvs_p: returns flat list of protein hgvs strings from variants
        + seqvars: returns flat list of SequenceVariant objects from variants
        
        Methods
        -------
        
        + to_dict(): returns non-underscored attributes (seqvar, hgvs_text, transcripts, seqvars) as dictionary
        + to_json(): returns a serialized JSON string representation of the object which can be used to instantiate this LVG again.
        + from_json(json_str): takes serialized JSON representation of this object and rebuilds LVG from its details.
        
        VariantComponents: Parsing and "Slang"
        ======================================
        
        `VariantComponents` allows instantiation in two different ways: using an hgvs.SequenceVariant object
        and using a set of components as keyword arguments.
        
        Usage starting from a SequenceVariant object::
        
            comp = VariantComponents(seqvar)
        
        Usage starting from individual components::
        
            comp = VariantComponents(seqtype='c', edittype='SUB', pos='322', ref='C', alt='T')
        
        Usage starting from "aminochange" string::
        
            comp = VariantComponents(aminochange='V777A')
            comp = VariantComponents(aminochange='Leu653Gly')
        
        (If starting with "aminochange" string, the `seqvar` and `edittype` attributes will be None.)
        
        If no seqtype is supplied, VariantComponents tries to infer the sequence type heuristically (e.g. the presence
        of a "U" in the ref or the alt implies this is an RNA string).
        
        VariantComponents may raise a `RejectedSeqVar` exception during instantiation (see "Exceptions" below).
        
        A VariantComponents object provides access to the following attributes and properties::
            
           seqtype: the sequence type of this seqvar (one of 'c', 'g', 'g', 'n')
           edittype: the type of mutation represented by this variant ('SUB', 'DEL', 'FS', etc)
           pos: position of the edit
           ref: reference sequence at given position (aka "wildtype")
           alt: alternate (or "mutant") at given position
        
           posedit: returns the HGVS "official" construction of this seqvar's position + edit information.
           posedit_slang: returns a list of algorithmically generated "slang" for given seqvar's posedit.
        
        
        Exceptions
        ==========
        
        All exceptions can be found and imported from metavariant.exceptions.
        
        `CriticalHgvsError`: raised when input HGVS string fails to instantiate a SequenceVariant object within the VariantLVG object.
        
        `RejectedSeqVar`: raised inside VariantComponents when input sequence components fail certain tests of completeness. For example, a protein seqvar will throw this Exception if the protein effect string is only a "?" (i.e. unknown protein effect).  A "SUB" (substitution) will fail the completeness test if an "alt" is not provided in the instantiated components.
        
        
        Setting UTA Server
        ==================
        
        When you find yourself outgrowing the public UTA server, you may want to install your own UTA server. 
        The instructions can be found on the [biocommons/uta repository README](https://bitbucket.org/biocommons/uta). Both "installing from database dumps" 
        and installing from docker have been tested working with metavariant.
        
        *How to Set UTA Host Variables*
        
        metavariant connects to a UTA server as soon as it is imported, so reconfiguring which UTA server is used
        happens at the environment variable level.  The relevant variables::
        
            UTA_HOST (default: 'default')
            UTA_PORT (default: 5432)
            UTA_USER (default: 'uta_admin')
            UTA_PASS (default: 'uta_admin')
            UTA_SCHEMA (default: 'uta_20150903')
            UTA_TIMEOUT (default: 3) -- how long to wait before giving up on a connection
        
        When you set up your own postgres server for the UTA database and you connect on the same server, the only
        environment variable you probably need to change is `UTA_HOST` (set it to "localhost").
        
        You may have to do more postgres administration to get your preferred configuration going, which is outside the scope of this README.
        
        
        Support and Maintenance
        =======================
        
        This library was developed in-house at Text2Gene, LLC.
        
        It is provided to the community free of charge by way of the Apache 2.0 License.
        
        You are free to modify it for commercial and non-commercial uses; just don't try to sell it as-is.
        
        Contributions, extensions, bug reports, suggestions, and swear words all happily accepted, 
        in that order.
        
        naomi@text2gene.com
        2016 and onwards
        
        
Platform: UNKNOWN
Description-Content-Type: text/x-rst
