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[ Source: gfapy  ]

Package: python3-gfapy (1.1.0+dfsg-1)

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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.

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Architecture Package Size Installed Size Files
alpha (unofficial port) 73.9 kB488.0 kB [list of files]
amd64 73.9 kB488.0 kB [list of files]
arm64 73.9 kB488.0 kB [list of files]
armel 73.9 kB488.0 kB [list of files]
armhf 73.9 kB488.0 kB [list of files]
hppa (unofficial port) 73.9 kB488.0 kB [list of files]
i386 73.9 kB488.0 kB [list of files]
m68k (unofficial port) 73.9 kB488.0 kB [list of files]
mips64el 73.9 kB488.0 kB [list of files]
mipsel 73.9 kB488.0 kB [list of files]
ppc64 (unofficial port) 73.9 kB488.0 kB [list of files]
ppc64el 73.9 kB488.0 kB [list of files]
riscv64 (unofficial port) 73.9 kB488.0 kB [list of files]
s390x 73.9 kB488.0 kB [list of files]
sh4 (unofficial port) 73.9 kB488.0 kB [list of files]
sparc64 (unofficial port) 73.9 kB488.0 kB [list of files]
x32 (unofficial port) 73.9 kB488.0 kB [list of files]