from dna_features_viewer import GraphicFeature, GraphicRecord
import pprint
from BCBio import GFF
from dna_features_viewer import BiopythonTranslator
import matplotlib as mpl
from matplotlib import pyplot as plt
filelist = os.listdir()
gffinput = [file for file in filelist if file.endswith(".gff")]
mpl.rcParams['font.family'] = "Times new roman"
mpl.rc('xtick', labelsize=5)
class CustomTranslator(BiopythonTranslator):
label_fields = ["label", "note", "name", "gene"]
for file in gffinput:
fig, ax = plt.subplots()
gff_records = []
file2 = open(file)
for rec in GFF.parse(file2):
gff_records.append(rec)
else:
file2.close()
for line in startend:
if str(file) in str(line):
start = int(line.split("\t")[1])
end = int(line.split("\t")[2].split("\n")[0])
record = translator.translate_record(gffrecords[0][start:end])
ax, = record.plot(figure_width=13, strand_in_label_threshold=7)
ax.figure.savefig(f"{file}.svg", bbox_inches="tight")`
Hi,
I got some problem to visualize my plot
here is my code
`# plot makeing
from dna_features_viewer import GraphicFeature, GraphicRecord import pprint from BCBio import GFF from dna_features_viewer import BiopythonTranslator import matplotlib as mpl from matplotlib import pyplot as plt
filelist = os.listdir() gffinput = [file for file in filelist if file.endswith(".gff")]
mpl.rcParams['font.family'] = "Times new roman" mpl.rc('xtick', labelsize=5)
class CustomTranslator(BiopythonTranslator): label_fields = ["label", "note", "name", "gene"]
translator = CustomTranslator()
for file in gffinput: fig, ax = plt.subplots() gff_records = [] file2 = open(file) for rec in GFF.parse(file2): gff_records.append(rec) else: file2.close() for line in startend: if str(file) in str(line): start = int(line.split("\t")[1]) end = int(line.split("\t")[2].split("\n")[0]) record = translator.translate_record(gffrecords[0][start:end]) ax, = record.plot(figure_width=13, strand_in_label_threshold=7) ax.figure.savefig(f"{file}.svg", bbox_inches="tight")`
after blank plot coming...
Thank you.
I attach my one gff file.
IPGI_1 CDS IP 515265 537111 . + 0 IPGI_1 IPGI_2 CDS IP 671625 676541 . + 0 IPGI_2 IPGI_3 CDS IP 1054545 1062076 . + 0 IPGI_3 AHGI1 CDS AH 140000 145000 . + 0 AHGI1 AHGI2 CDS AH 217500 222500 . + 0 AHGI2 AHGI3 CDS AH 517500 537500 . + 0 AHGI3 AHGI4 CDS AH 670000 677500 . + 0 AHGI4 AHGI5 CDS AH 1237500 1242500 . + 0 AHGI5 AHGI6 CDS AH 1745000 1750000 . + 0 AHGI6 AHGI7 CDS AH 1830000 1837500 . + 0 AHGI7 AHGI8 CDS AH 2245000 2250000 . + 0 AHGI8 AHGI9 CDS AH 2682500 2697500 . + 0 AHGI9 AHGI10 CDS AH 3062500 3067500 . + 0 AHGI10 AHGI11 CDS AH 3092500 3105000 . + 0 AHGI11 AHGI12 CDS AH 3107500 3115000 . + 0 AHGI12 AHGI13 CDS AH 3125000 3130000 . + 0 AHGI13 AHGI14 CDS AH 3170000 3177500 . + 0 AHGI14 AHGI15 CDS AH 3185000 3195000 . + 0 AHGI15 AHGI16 CDS AH 3275000 3280000 . + 0 AHGI16