How can I make a dataset?

[kdhjk1]

Loading dataset is the first start of pygenomeviz of API.
How can I make dataset with gbk files and links?
And please write the practical loading procedures for jupyter notebook.

[moshi4]

The procedure for visualizing multiple Genbank files and MUMmer comparison link results is described as jupyter notebooks in the following document.
https://moshi4.github.io/pyGenomeViz/getting_started/#2-4-genome-alignment-visualization-workflow

The source code of pgv-mummer and pgv-mmseqs CLI may also help you understand the dataset preparation procedure.

[kdhjk1]

[moshi4]

I tried some scripts and have a question now for the pygenomeviz.
Can I draw the figure for the selected range like the Gallery Example. 3. Enterobacteria phage

Genome selected regions can be plotted by setting min_range and max_range in the Genbank parser class and the option start_pos(=gbk.min_range) in the add_feature_track function.

Below is an example code that plots only NC_019724 and NC_013600 selected regions among multiple genomes.

from pygenomeviz import Genbank, GenomeViz, load_dataset

gv = GenomeViz(
    fig_width=10,
    fig_track_height=0.5,
    feature_track_ratio=0.5,
    tick_track_ratio=0.5,
    align_type="center",
    tick_style="bar",
    tick_labelsize=10,
)

gbk_files, links = load_dataset("enterobacteria_phage")
for idx, gbk_file in enumerate(gbk_files):
    if idx in (0, 3):  
        # Limit NC_019724, NC_013600 plot genomic range (10,000 - 30,000 bp)
        gbk = Genbank(gbk_file, min_range=10000, max_range=30000)
    else:
        gbk = Genbank(gbk_file)

    track = gv.add_feature_track(gbk.name, size=gbk.range_size, start_pos=gbk.min_range, labelsize=10)
    track.add_genbank_features(
        gbk,
        label_type="product" if idx == 0 else None,  # Labeling only top track
        label_handle_func=lambda s : "" if s.startswith("hypothetical") else s,  # Ignore 'hypothetical ~~~' label
        labelsize=8,
        labelvpos="top",
        facecolor="skyblue",
        linewidth=0.5,
        labelrotation=45,
    )
    track.set_sublabel(size=8)

fig = gv.plotfig()

Whole genome drawing is working but it is not working with some error messages such as self.start & self.end.

If you provide me the code in which the error occurred, I will be able to give you more specific advice.

[kdhjk1]

The drawing with whole genome is possible.
Error message when drawing whole genome with range option (ex. min_range=10000, max_range=25000)

Can I draw some link lines with selected ranges with genome sequence, not the whole range?

pygenomeviz error question.odt
figure .pdf

[moshi4]

Since you have not presented the source code, I do not know the cause of the error.
However, it is possible to compare and visualize the specified range genomes with the CLI of pgv-mummer and pgv-mmseqs, but did you try it?

Here is an example of CLI.

# Download test dataset
pgv-download-dataset -n enterobacteria_phage
# Compare & visualize 3 species genome with range in 10000 - 25000 bp
pgv-mummer --gbk_resources NC_019724.gbk:10000-25000 NC_024783.gbk:10000-25000 NC_016566.gbk:10000-25000 -o mummer_example

If you want a more custom pgv-mummer output figure from the API, you can modify the source in src/pygenomeviz/mummer.py. The pgv-mummer command is synonymous with python mummer.py.

[kdhjk1]

Thank you very much! I will try it.

And, I think it would be so good to draw the figure in page 2 of the attached pygenomeviz error question.odt file?
The whole genome can be drawn with some complicated labels, but it may cause error when I tried it with range limits (page 3).

[moshi4]

Oh, sorry, I overlooked the fact that the ODT file has multiple pages.

It seems to me that the error is due to an incorrectly specified argument in the gv.add_feature_track method on line 26.

Try changing the source code as follows.

# Before Change (line 26)
track = gv.add_feature_track(gbk.name, gbk.range_size, labelsize=10)

# After Change (line 26)
track = gv.add_feature_track(gbk.name, size=gbk.range_size, start_pos=gbk.min_range, labelsize=10)

This would resolve the error that is currently being displayed.

---

I think that even after resolving the above error, there is still a possibility that the gv.add_link method may cause an error.
If the error occurs in the gv.add_link method, please try the following source code change.

# Before Change (line 43)
gv.add_link(link_data1, link_data2, ...)

# After Change (line 43)
try:
    gv.add_link(link_data1, link_data2, ...)
except ValueError:
    # Ignore links outside the illegal range
    pass