GFF plot doesnt work

[ZarulHanifah]

Hello DnaFeaturesViewer developers,

I can't plot my gff (attached, had to change extension to txt ATCC_13124.gff.txt). There is supposed to be 2997 features, but only 1 record was produced from GFF.parse().

[veghp]

Thank you for your interest in DnaFeaturesViewer. I had a look at your GFF file and it indeed contains only one record (which is 3.2M bp long) with 2997 features.

What is your expected outcome? I made a smaller version of the file (containing the first 5 features) and it plots fine:

[ZarulHanifah]

Amazing! What is the code to plot that? It is much simpler with genbank files, but from the tutorial, it wasn't clear how to start from GFF.parse() to get to the plot.

Please show me the code, pleaseee.

Thank you.

[veghp]

If you have a small GFF file, you can run:

from dna_features_viewer import BiopythonTranslator
graphic_record = BiopythonTranslator().translate_record("yourfile.gff")
ax, _ = graphic_record.plot(figure_width=10, strand_in_label_threshold=7)

If you want to plot only a section of the record (from start to end):

from dna_features_viewer import BiopythonTranslator
from BCBio import GFF
in_file = "ATCC_13124.gff"

in_handle = open(in_file)
gff_records = []
for rec in GFF.parse(in_handle):
    print(rec)
    gff_records.append(rec)
in_handle.close()

start = 0
end = 5000
record = BiopythonTranslator().translate_record(gff_records[0][start:end])
ax, _ = record.plot(figure_width=10, strand_in_label_threshold=7)

Note that GFF.parse() is part of the BCBio package, not Dna Features Viewer.

[ZarulHanifah]

fig, ax = plt.subplots()

gff_path = "results/ALL_PROKKA/ATCC_13124/ATCC_13124.gff"

gff_records = []

with open(gff_path) as in_handle:
    for rec in GFF.parse(in_handle):
        gff_records.append(rec)
        
start, end = 0, 5000
record = BiopythonTranslator().translate_record(gff_records[0][start:end])
record.plot(ax= ax)

Beautiful! Thank you!!