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Bug#869969: ITP: gfapy -- flexible and extensible software library for handling sequence graphs




Package: wnpp
Severity: wishlist
Owner: Sascha Steinbiss <satta@xxxxxxxxxx>

* Package name    : gfapy
  Version         : 1.0.0
  Upstream Author : Giorgio Gonnella
* URL             : https://github.com/ggonnella/gfapy
* License         : ISC
  Programming Lang: Python
  Description     : flexible and extensible software library for handling sequence graphs

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 the user to easily combine different sequence analysis tools.

This library implements the GFA1 and GFA2 specification. It is possible 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 one 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.