Annotations problem #4
Description
Hi Damien,
It is my first time using your script for annotating my bacterial FASTA sequence. From the console of my python (3.8) on Ubuntu/Linux 20.10, I see the script stuck with Aragon. I updated all dependencies; however, I still get the same error.
""
Traceback (most recent call last):
File "", line 11, in
featdf,recs = pathogenie.app.run_annotation(infile, threads=10, kingdom='bacteria')
File "/home/ahmed/src/pathogenie/pathogenie/app.py", line 461, in run_annotation
arag = aragorn(infile)
File "/home/ahmed/src/pathogenie/pathogenie/app.py", line 333, in aragorn
df = tools.read_aragorn(outfile)
File "/home/ahmed/src/pathogenie/pathogenie/tools.py", line 841, in read_aragorn
if m.group(1):
AttributeError: 'NoneType' object has no attribute 'group'
"""
#######################################################
This error refers to this chunk specifically in tools.py script
m = re.match('(c*)[(\d+),(\d+)]', cols[2])
if m:
start = int(m.group(2)) - 1
end = int(m.group(3))
if m.group(1): #here I change
rstrand = -1
else:
rstrand = 1
res.append([contig, name, feat_type, start, end, anticodon, rstrand])
#######################################################
Any advice for fixing this issue?
Ps: I tried using the GUI and no output for annotation work.
Thanks in advance.