FASTG is a format for describing sequencing assembly graphs. It is 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The latest specification for the FASTG format is version 1.00, as of writing; the original FASTG website is down, but an archived version of the v1.00 specification is accessible here. Whenever the rest of this documentation mentions "the FASTG spec," this is in reference to this version of the specification.
pyfastg is a Python library designed to parse graphs that follow a subset of the FASTG spec. In particular, pyfastg is designed to work with files output by the SPAdes family of assemblers.
The pyfastg library contains parse_fastg(), a function that
takes as input a path to a SPAdes FASTG file. parse_fastg() reads this
FASTG file and returns a NetworkX
DiGraph object representing the structure of the assembly graph.
pyfastg is useful as a starting point for other applications.
Using this NetworkX DiGraph object, we can do whatever we want with the
assembly graph: analyze it, convert it to other formats, visualize it, etc.
The FASTG spec contains the following sentence (in section 6, page 7):
Note also that strictly speaking, [the structure described in a FASTG file] is not a graph at all, as we have not specified a notion of vertex. However in many cases one can without ambiguity define vertices and thereby associate a bona fide digraph, and we do so frequently in this document to illustrate concepts.
We use the following approach to get around this problem: "edges" in the FASTG file will be represented as nodes in the NetworkX graph produced by pyfastg, and "adjacencies" between edges in the FASTG file will be represented as edges in the NetworkX graph produced by pyfastg.
As far as we're aware, this "conversion" from edges to nodes matches how FASTG files have often been visualized in the past.
pyfastg can be installed using pip or conda:
pip install pyfastgconda install -c bioconda pyfastgAs of writing, pyfastg's only direct dependency (which should be installed automatically when running either of the above installation commands) is NetworkX. pyfastg requires a minimum NetworkX version of 2.
As of writing, pyfastg supports Python 3.6 and up. pyfastg might be able to work with earlier versions of Python, but we do not explicitly test against these.
The second line (which points to one of pyfastg's test assembly graphs) assumes that you're located in the root directory of the pyfastg repo.
>>> 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 sequences in this graph (these are "edges" in the FASTG
>>> # file, but are represented as 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 sequence (length, coverage, 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-'}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 edge names are not supported.
Each edge in the file must have a name formatted like:
EDGE_1_length_9909_cov_6.94721The edge ID (here, 1) can contain the characters a-z, A-Z, and 0-9.
The edge length (here, 9909) can contain the characters 0-9.
The edge coverage (here, 6.94721) can contain the characters 0-9 and ..
An edge name can optionally end with a ' character, indicating that
this edge is a reverse complement. We will refer to whether or not an edge name
ends with ' as its orientation: an edge that does not end with a ' has a
+ orientation, and an edge name that ends with a ' has a - orientation.
All edge names in a FASTG file should be consistent with respect to a given
ID and orientation.
If, in a single FASTG file, pyfastg sees a reference to an edge named
EDGE_1_length_9909_cov_6.94721 and also a reference to an edge named
EDGE_1_length_9908_cov_6.95 (with the same ID [1]
and orientation [+], but a different length and/or coverage)
then it will throw an error.
Here, we refer to each line starting with > as an edge declaration. An
edge's sequence is described in the line(s) following its edge declaration
(until the next edge declaration); additionally, the outgoing adjacencies from
this edge to other edges may be described on this line, if present. For example,
the line
>EDGE_1_length_5_cov_10:EDGE_2_length_3_cov_1,EDGE_3_length_6_cov_2.5',EDGE_4_length_8_cov_5.1;
indicates that the edge EDGE_1_length_5_cov_10 has three outgoing adjacencies: to the
edges EDGE_2_length_3_cov_1, EDGE_3_length_6_cov_2.5', and EDGE_4_length_8_cov_5.1.
This line would thus result in three "edges" being created
in the NetworkX graph produced by pyfastg: (1+ → 2+), (1+ → 3-), and (1+ → 4+).
Each edge declaration must end with a ; character (after removing trailing
whitespace). Section 15 of the FASTG spec mentions that having a newline
after the semicolon isn't required, but we require it here for the sake of
simplicity.
We assume that each sequence (the line(s) between edge declarations)
consists only of the characters A, C, G, T, or U. So, more complex
types of strings (e.g. the "stuffed gaps" described in the FASTG spec) are
not allowed in an edge's sequence.
Additionally, lowercase characters or degenerate nucleotides are not allowed;
this matches section 15 of the FASTG spec.
The FASTG spec doesn't explicitly allow for uracil (U), but we allow it
anyway in order to support RNA sequences. (U and T are allowed to be contained
in the same sequence,
in the unlikely case that this is needed.)
Leading and trailing whitespace in sequence lines will be ignored, as will blank lines within a sequence. So, something like
>EDGE_1_length_4_cov_100;
ATC
G
is technically valid: this sequence is read as ATCG.
However, the following example:
>EDGE_1_length_4_cov_100;
ATC G
is not valid and will cause pyfastg to throw an error.
This is because the inner space between
the C and the G would be read as part of the sequence.
Nodes in the returned DiGraph (corresponding to edges in the FASTG file)
will contain three attribute fields:
length: the length of the sequence (represented as a pythonint)cov: the coverage of the sequence (represented as a pythonfloat)gc: the GC-content (in the range [0, 1]) of the sequence (represented as a pythonfloat)
Each node's name is a python str created by concatenating edge IDs and orientations.
For example, EDGE_1_length_9909_cov_6.94721 will correspond to a node named 1+.
This naming scheme is analogous to that used by
Bandage.
pyfastg only creates nodes based on the edges
explicitly described in the FASTG file. If a file only describes edges
EDGE_1_length_5_cov_10, EDGE_2_length_6_cov_10', and EDGE_3_length_7_cov_15, then
pyfastg will only create nodes 1+, 2-, and 3+, and not the reverse complement
nodes 1-, 2+, 3-, etc.
Similarly, if a file contains an adjacency from edge EDGE_1_length_5_cov_10 to
EDGE_2_length_6_cov_10', then this adjacency will only be represented as a single edge
(1+ → 2-) in pyfastg's output graph. The implied reverse-complement of this
edge (2+ → 1-) will not be created unless the file explicitly
contains an adjacency from EDGE_2_length_6_cov_10 to EDGE_1_length_5_cov_10'.
Pull requests are welcome! If you're interested in developing pyfastg's code, this section provides some instructions for getting started.
You will probably want to fork this repository and then clone your fork to your
computer. Once you do this, cd into the root of the repository and run
pip install -e .[dev]to install pyfastg in "editable mode." Thanks to the [dev] flag, this will also install
pyfastg's development dependencies (see the extras_require line in
setup.py for details).
pyfastg's Makefile
contains targets that perform these three tasks:
- Run tests:
make test - Lint and style-check the code:
make stylecheck - Automatically style the code:
make style
These targets should all be run from the root of the pyfastg repository. They should hopefully be self-explanatory, but let us know if you have any questions.
See pyfastg's
CHANGELOG.md file
for information on the changes included with new pyfastg releases.
pyfastg is licensed under the MIT License. Please see pyfastg's
LICENSE file for details.
The recommended way to get in touch with pyfastg's developers is by opening a GitHub issue.