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Minimal Python library for parsing SPAdes FASTG files

Project description

pyfastg: a minimal Python library for parsing networks from SPAdes FASTG files

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The FASTG file format

FASTG is a format to describe genome assemblies, geared toward accurately representing the ambiguity resulting from sequencing limitations, ploidy, or other factors that complicate representation of a seqence as a simple string. The official spec for the FASTG format can be found here.

pyfastg parses graphs that follow a subset of this specification: in particular, it is designed to work with files output by the SPAdes family of assemblers.

pyfastg

pyfastg contains parse_fastg(), a function that accepts as input a path to a SPAdes FASTG file. This function parses the structure of the specified file, returning a NetworkX DiGraph object representing the structure of the graph.

pyfastg is very much in its infancy, so it may be most useful as a starting point. Pull requests welcome!

Quick Example

>>> import pyfastg
>>> g = pyfastg.parse_fastg("pyfastg/tests/input/assembly_graph.fastg")
>>> # g is now a NetworkX DiGraph! We can do whatever we want with this object.
>>> # Example: List the nodes in g
>>> g.nodes()
NodeView(('1+', '29-', '1-', '6-', '2+', '26+', '27+', '2-', '3+', '4+', '6+', '7+', '3-', '33-', '9-', '4-', '5+', '5-', '28+', '7-', '8+', '28-', '9+', '8-', '12-', '10+', '12+', '10-', '24-', '32-', '11+', '30-', '11-', '27-', '19-', '13+', '25+', '31-', '13-', '14+', '14-', '26-', '15+', '15-', '23-', '16+', '16-', '17+', '17-', '19+', '18+', '33+', '18-', '20+', '20-', '22+', '21+', '21-', '22-', '23+', '24+', '25-', '29+', '30+', '31+', '32+'))
>>> # Example: Get details for a single node (length, coverage, and GC-content)
>>> g.nodes["15+"]
{'length': 193, 'cov': 6.93966, 'gc': 0.5492227979274611}
>>> # Example: Get information about the graph's connectivity
>>> import networkx as nx
>>> components = list(nx.weakly_connected_components(g))
>>> for c in components:
...     print(len(c), "nodes")
...     print(c)
...
33 nodes
{'8-', '17-', '15+', '30+', '16+', '26-', '25+', '19+', '7+', '23+', '14-', '18-', '10-', '29-', '20-', '27-', '11-', '5-', '3+', '2-', '12-', '13+', '31-', '6+', '1+', '21-', '24-', '32-', '22+', '28+', '4+', '33-', '9-'}
33 nodes
{'26+', '29+', '18+', '3-', '2+', '8+', '15-', '24+', '9+', '17+', '27+', '28-', '11+', '6-', '20+', '14+', '19-', '13-', '4-', '21+', '5+', '31+', '22-', '12+', '25-', '30-', '10+', '1-', '7-', '32+', '23-', '33+', '16-'}

Required File Format (tl;dr: SPAdes-dialect FASTG files only)

Currently, pyfastg is hardcoded to parse FASTG files created by the SPAdes assembler. Other valid FASTG files that don't follow the pattern used by SPAdes for node names are not supported.

In particular, each node in the file must be declared as

>EDGE_1_length_9909_cov_6.94721

The node ID (here, 1) can contain the characters a-z, A-Z, and 0-9.

The node length (here, 9909) can contain the characters 0-9.

The node coverage (here, 6.94721) can contain the characters 0-9 and ..

We assume that each node sequence (the line(s) between node declarations) consists only of valid DNA characters, as determined by skbio.DNA. Leading and trailing whitespace in sequence lines will be ignored, so something like

    ATC

 G     

is perfectly valid (however, ATC G is not since the inner space, , will be considered part of the sequence).

It is also worth noting that pyfastg only creates nodes/edges based on those observed in the graph: if your graph only contains nodes 1+, 2+, and 3+, then this won't automatically create reverse complement nodes 1-, 2-, 3-, etc.

Identified node attributes

Nodes in the returned DiGraph (represented in the FASTG file as EDGE_s) contain three attribute fields:

  1. length: the length of the node (represented as a python int)
  2. cov: the coverage of the node (represented as a python float)
  3. gc: the GC-content of the node's sequence (represented as a python float)

Furthermore, every node's name will end in - if the node is a "reverse complement" (i.e. if its declaration in the FASTG file ends in a ' character) and + otherwise.

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