1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 | Gfapy ~~~~~ |travis| |readthedocs| |latesttag| |license| |requiresio| |bioconda| |pypi| |debian| |ubuntu| .. sphinx-begin 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 3.7. 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). It is also available as a package in some Linux distributions (Debian, Ubuntu). 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, a 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 .. sphinx-end .. |travis| image:: https://travis-ci.org/ggonnella/gfapy.svg?branch=master :target: https://travis-ci.org/ggonnella/gfapy :alt: Travis .. |latesttag| image:: https://img.shields.io/github/v/tag/ggonnella/gfapy :target: https://github.com/ggonnella/gfapy/tags :alt: Latest GitHub tag .. |readthedocs| image:: https://readthedocs.org/projects/pip/badge/?version=stable :target: https://pip.pypa.io/en/stable/?badge=stable :alt: ReadTheDocs .. |bioconda| image:: https://img.shields.io/conda/vn/bioconda/gfapy :target: https://bioconda.github.io/recipes/gfapy/README.html :alt: Bioconda .. |pypi| image:: https://img.shields.io/pypi/v/gfapy :target: https://pypi.org/project/gfapy/ :alt: PyPI .. |debian| image:: https://img.shields.io/debian/v/gfapy :target: https://packages.debian.org/search?keywords=gfapy :alt: Debian .. |ubuntu| image:: https://img.shields.io/ubuntu/v/gfapy :target: https://packages.ubuntu.com/search?keywords=gfapy :alt: Ubuntu .. |license| image:: https://img.shields.io/pypi/l/gfapy :target: https://github.com/ggonnella/gfapy/blob/master/LICENSE.txt :alt: ISC License .. |requiresio| image:: https://requires.io/github/ggonnella/gfapy/requirements.svg?branch=master :target: https://requires.io/github/ggonnella/gfapy/requirements/?branch=master :alt: Requirements Status |
Commit History @2150ff2b-6bdf-4ab0-9a41-f577df5071a7/main
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- Update metadata with ref to conda Steffen Möller 4 years ago
- d/u/metadata: yamllint Steffen Moeller 4 years ago
- Updated d/u/metadata Steffen Möller 5 years ago
- Upload to unstable Andreas Tille 5 years ago
- Do not parse d/changelog Andreas Tille 5 years ago
- Less parsing of d/changelog, Binary package in section python Andreas Tille 5 years ago
- Drop unneeded Testsuite field Andreas Tille 5 years ago
- Standards-Version: 4.2.1 Andreas Tille 5 years ago
- Point Vcs fields to salsa.debian.org Andreas Tille 5 years ago
- debhelper 11 Andreas Tille 5 years ago
- Remove invalid fields from debian/upstream/metadata Andreas Tille 6 years ago
- fix d/upstream/metadata Sascha Steinbiss 6 years ago
- add override for false positive in Lintian Sascha Steinbiss 6 years ago
- dch -r Sascha Steinbiss 6 years ago
- add ITP number Sascha Steinbiss 6 years ago
- add preprint paper metadata Sascha Steinbiss 6 years ago
- finish packaging Sascha Steinbiss 6 years ago
- add man pages Sascha Steinbiss 6 years ago
- reword long description Sascha Steinbiss 6 years ago
- fix grammar Sascha Steinbiss 6 years ago
- override test for now Sascha Steinbiss 6 years ago
- reset to UNRELEASED Sascha Steinbiss 6 years ago
- initial packaging Sascha Steinbiss 6 years ago
- New upstream version 1.0.0+dfsg Sascha Steinbiss 6 years ago
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