Metadata-Version: 1.1
Name: gfapy
Version: 1.0.0
Summary: Library for handling data in the GFA1 and GFA2 formats
Home-page: https://github.com/ggonnella/gfapy
Author: Giorgio Gonnella and others (see CONTRIBUTORS)
Author-email: gonnella@zbh.uni-hamburg.de
License: ISC
Description: The Graphical Fragment Assembly (GFA) are formats for the representation
        of sequence graphs, including assembly, variation and splicing graphs.
        Two versions of GFA have been defined (GFA1 and GFA2) and several sequence
        analysis programs have been adopting the formats as an interchange format,
        which allow to easily combine different sequence analysis tools.
        
        This library implements the GFA1 and GFA2 specification
        described at https://github.com/GFA-spec/GFA-spec/blob/master/GFA-spec.md.
        It allows to create a Gfa object from a file in the GFA format
        or from scratch, to enumerate the graph elements (segments, links,
        containments, paths and header lines), to traverse the graph (by
        traversing all links outgoing from or incoming to a segment), to search for
        elements (e.g. which links connect two segments) and to manipulate the
        graph (e.g. to eliminate a link or a segment or to duplicate a segment
        distributing the read counts evenly on the copies).
        
        The GFA format can be easily extended by users by defining own custom
        tags and record types. In Gfapy, it is easy to write extensions modules,
        which allow to define custom record types and datatypes for the parsing
        and validation of custom fields. The custom lines can be connected, using
        references, to each other and to lines of the standard record types.
        
        Requirements
        ~~~~~~~~~~~~
        
        Gfapy has been written for Python 3 and tested using Python version 3.3.
        It does not require any additional Python packages or other software.
        
        Installation
        ~~~~~~~~~~~~
        
        Gfapy is distributed as a Python package and can be installed using
        the Python package manager pip, as well as conda (in the Bioconda channel).
        
        The following command installs the current stable version from the Python
        Packages index::
        
          pip install gfapy
        
        If you would like to install the current development version from Github,
        use the following command::
        
          pip install -e git+https://github.com/ggonnella/gfapy.git#egg=gfapy
        
        Alternatively it is possible to install gfapy using conda. Gfapy is
        included in the Bioconda (https://bioconda.github.io/) channel::
        
          conda install -c bioconda gfapy
        
        Usage
        ~~~~~
        
        If you installed gfapy as described above, you can import it in your script
        using the conventional Python syntax::
        
          >>> import gfapy
        
        Documentation
        ~~~~~~~~~~~~~
        
        The documentation, including this introduction to Gfapy, an user manual
        and the API documentation is hosted on the ReadTheDocs server,
        at the URL http://gfapy.readthedocs.io/en/latest/ and it can be
        downloaded as PDF from the URL
        https://github.com/ggonnella/gfapy/blob/master/manual/gfapy-manual.pdf.
        
        References
        ~~~~~~~~~~
        
        Giorgio Gonnella and Stefan Kurtz "GfaPy: a flexible and extensible software
        library for handling sequence graphs in Python", Bioinformatics (2017) btx398
        https://doi.org/10.1093/bioinformatics/btx398
        
Keywords: bioinformatics genomics sequences GFA assembly graphs
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: ISC License (ISCL)
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
