Comments (4)
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.
from dnafeaturesviewer.
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:
from dnafeaturesviewer.
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.
from dnafeaturesviewer.
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!!
from dnafeaturesviewer.
Related Issues (20)
- Cannot apply sequence translation on plot_on_multiple_lines or plot_on_multiple_pages HOT 2
- BiopythonTranslator: SeqFeatures with location_operator='join' get wrong position
- Labels overlap whan sharing axis HOT 2
- Feature request: x_lim best-fit HOT 6
- Enhanced Bokeh support for multiple plots HOT 2
- Linking exon annotations with intron lines, and other things. HOT 5
- Add an example which plots sequence features not starting from 0 HOT 5
- truncated scaffolds from gff files HOT 4
- figure is not coming
- type hints support HOT 1
- Error on BioPython v1.8.0 HOT 9
- type error for global variable related to BioPython update HOT 2
- sequences display from 1 not 0 ? HOT 1
- How to solve the memory problem of batch plotting? HOT 3
- Overlapping arrows in circular DNA HOT 1
- CircularGraphicRecord does not work. Unable to make circular graphs HOT 1
- UndefinedSequenceError with gff files and BioPython 1.81
- Oval or diamond/octagon in addition to arrows for displayed features? HOT 1
- 'Seq' object has no attribute 'defined' HOT 2
- feature location in a join, how to correnctly translate HOT 3
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from dnafeaturesviewer.