separate gfapy from RGFA

.gitignore

@@ -1,18 +1,5 @@
-*.gem
-.yardoc
 doc
-gfapy_doc/_build
-doc/_build
-pdfdoc/index.html
-pdfdoc/rgfa*.pdf
-pdfdoc/cover.html
-cheatsheet/*.aux
-cheatsheet/*_latexmk
-cheatsheet/*.fls
-cheatsheet/*.log
-cheatsheet/*.pdf
-cheatsheet/version
-manual/manual.pdf
+
 # Compiled python modules
 *.pyc
 
@@ -22,3 +9,6 @@ manual/manual.pdf
 # Python egg metadata, regenerated from source files by setuptools
 /*.egg-info
 /*.egg
+
+# Wheel data
+build

CHANGELOG

@@ -1,60 +1,3 @@
-== GFA2 ==
-
-- Trace alignments
-- Custom record types
-- More precise fields terminology:
--- required fields => positional fields
--- optional fields => tags
-
-== HEAD ==
-
-- improve handling of comment lines
-  (now: stored in RGFA object; edit, deletion, output)
-
-== 1.3.1 ==
-
-- fix: add file missing from gemspec
-
-== 1.3 ==
-
-major changes:
-- changes in GFA specification:
--- P lines: cigars field is now overlaps
--- comment lines
--- forbid +, and -, in segment names
-- .rb suffix removed from bin/* scripts
-
-minor changes:
-- improved links terminology
-  (normal link -> canonical; reverse link/CIGAR -> complement)
-- definition of canonical link simplified
-
-== 1.2.1 ==
-
-- support new segment tags SH and UR
-- update cheatsheet
-
-== 1.2 ==
-
-- merge RGFATools into the main RGFA gem
-
-== 1.1 ==
-
-- performance and code organization improvements
-- Line code rewritten:
--- uses an Hash instead of Array for fields data
--- support lazy parsing of some field types
--- simpler code for subclasses
--- define a datatype for required fields
--- Field[Parser|Validator|Writer]
-- Optfield class replaced
-- use symbols instead of strings when appropriate
-
-== 1.0.1 ==
-
-- complete YARD documentation
-- remove redundant/unused code
-
-== 1.0 ==
+== 1.0.0 ==
 
 - initial release

CONTRIBUTORS

@@ -1,4 +1,6 @@
-The following contributors helped to develop RGFA. Please drop a note to
+The following contributors helped to develop gfapy. Please drop a note to
 gonnella@zbh.uni-hamburg.de if I left someone out or missed something.
 
+- Tim Weber (translation of parts of the code from Ruby to Python)
 - Stefan Kurtz (advises)
+

LICENSE

@@ -1,10 +1,10 @@
-All code of RGFA is released under the following ISC license.
+All code of gfapy is released under the following ISC license.
 It is functionally equivalent to a two-term BSD copyright with
 language removed that is made unnecessary by the Berne convention.
 See http://openbsd.org/policy.html for more information on copyrights.
 
-Copyright (c) 2016 Giorgio Gonnella and CONTRIBUTORS
-Copyright (c) 2016 Center for Bioinformatics, University of Hamburg
+Copyright (c) 2017 Giorgio Gonnella and CONTRIBUTORS
+Copyright (c) 2017 Center for Bioinformatics, University of Hamburg
 
 Permission to use, copy, modify, and distribute this software for any
 purpose with or without fee is hereby granted, provided that the above

Makefile

@@ -0,0 +1,31 @@
+default: tests
+
+.PHONY: manual tests
+
+PYTHON=python3
+PIP=pip3
+
+# Install using pip
+install:
+	${PIP} install . --upgrade --user
+
+# Source distribution
+sdist:
+	${PYTHON} setup.py sdist
+
+# Pure Python Wheel
+wheel:
+	${PYTHON} setup.py bdist_wheel
+
+# Create the manual
+manual:
+	cd manual; \
+		cat chapters | xargs pandoc -o gfapy-manual.pdf
+
+# Run unit tests
+tests:
+	${PYTHON} -m unittest discover
+
+# Remove distribution files
+cleanup:
+	rm -rf dist/ build/ gfapy.egg-info/

README.rst

@@ -1,2 +1,63 @@
-The README.md of RGFA should be translated in reStructuredText.
-Github supports both formats.
+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.
+
+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
+
+Usage
+=====
+
+If you installed gfapy as described above, you can import it in your script
+using the conventional Python syntax::
+
+  import gfapy
+
+Documentation
+=============
+
+An user manual is available at
+https://github.com/ggonnella/gfapy/blob/master/manual/gfapy-manual.pdf
+
+References
+==========
+
+The manuscript describing Gfapy has been submitted and is currently under
+review. This section will be updated, as soon as the publication is available.