dmnfarrell / pathogenie Goto Github PK

When highlighting a set of features in the feature table and right-clicking to "draw features", the slider location value in the interactive sequence feature viewer is not updated.

This means that the slider stays at position 1 in the currently viewed genome, so trying to zoom in and out from the current view resets the position to the start of the genome. Similarly, it means you can't pan to the left or right of the feature selection, because the location resets to the start of the genome.

When zooming, the slider position is read from start = int(self.slider.value()). I don't think this value is updated when using "draw features".

I'd suggest setting self.slider.value to the range for the currently viewed features. Something like
self.slider.setvalue(new_location) (I'd attempt to submit a patch myself, but I haven't really used github much so not sure how the process works!)

Thanks!

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.

The function annotation_files has a wrong filepath for output files. I think the best workaround is replace string "temp" with the variable outdir in the def annotation_files()

The functionclustal_alignment has get_cmd("clustalw") giving an error when running clustal. A tip is replace "clustalw" with "clustalw2".

I am having issues installing pygenefinder on my Macintosh machine (python 3.7.0), would you have any suggestion to resolve the issue?

pip install pygenefinder resulted in the following errors:

ERROR: Could not find a version that satisfies the requirement pygenefinder (from versions: none)
ERROR: No matching distribution found for pygenefinder

Kind regards