quadram-institute-bioscience / albatradis Goto Github PK

Hi,

Everything else seems to be working following conda installation. However, commands using graphviz seems to fail. Any idea how to solve this issue?

Thank you

:~$ albatradis-presence_absence -h
Traceback (most recent call last):
File "/home/phil/miniconda3/envs/py36/bin/albatradis-presence_absence", line 8, in
from albatradis.AlbaTraDISPresenceAbsence import AlbaTraDISPresenceAbsence
File "/home/phil/miniconda3/envs/py36/lib/python3.6/site-packages/albatradis/AlbaTraDISPresenceAbsence.py", line 6, in
from albatradis.PresenceAbsence import PresenceAbsence
File "/home/phil/miniconda3/envs/py36/lib/python3.6/site-packages/albatradis/PresenceAbsence.py", line 13, in
from graphviz import Digraph
ModuleNotFoundError: No module named 'graphviz'

:~$ albatradis-artemis_project -h
Traceback (most recent call last):
File "/home/phil/miniconda3/envs/py36/bin/albatradis-artemis_project", line 8, in
from albatradis.AlbaTraDISArtemisProject import AlbaTraDISArtemisProject
File "/home/phil/miniconda3/envs/py36/lib/python3.6/site-packages/albatradis/AlbaTraDISArtemisProject.py", line 3, in
from albatradis.ArtemisProject import ArtemisProject
File "/home/phil/miniconda3/envs/py36/lib/python3.6/site-packages/albatradis/ArtemisProject.py", line 7, in
from albatradis.PresenceAbsence import PresenceAbsence
File "/home/phil/miniconda3/envs/py36/lib/python3.6/site-packages/albatradis/PresenceAbsence.py", line 13, in
from graphviz import Digraph
ModuleNotFoundError: No module named 'graphviz'

If the data does't allow calculation of essentiality cut off, we need to provide better error message and continue the program.

Please update the documentation and/or command line output to make it clearer that albatradis-presence_absence should be run on multiple gene report files. If it is run on one then there is an exception as follows:-
raise ValueError("The number of observations cannot be determined on "
ValueError: The number of observations cannot be determined on an empty distance matrix.

This does not make it very clear to the user that they need to be running the command with more than one gene report files.

In https://github.com/quadram-institute-bioscience/albatradis/blob/master/setup.py version is set incorrectly:
...
version = 'x.y.z'
...

Hi, i've been trying to run AlbaTradis using both the example datasets and my own, but this error keeps popping up:

File "/Users/s2984406/opt/anaconda3/lib/python3.7/site-packages/Bio/GenBank/init.py", line 1424, in record_end
"Could not determine alphabet for seq_type %s" % self._seq_type
ValueError: Could not determine alphabet for seq_type linear unknown

Is there a way to rectify this? Thanks!

Having similar issues as #3 , specifically I am running albatradis -v -o OUTPUT emblfile condition_plots control_plots. This produces 7 files, without the gene_report.csv

When I run 'albatradis -v -a -o OUTPUT emblfile condition_plots control_plots', I get the following error messages:

Error in hist.default(ii, breaks = 200, plot = FALSE) :
'x' must be numeric
Calls: hist -> hist.default
Execution halted
Traceback (most recent call last):
File "/home/amy/anaconda3/bin/albatradis", line 63, in
albatradis.run()
File "/home/amy/anaconda3/lib/python3.7/site-packages/albatradis/AlbaTraDIS.py", line 54, in run
bi.run()
File "/home/amy/anaconda3/lib/python3.7/site-packages/albatradis/BlockInsertions.py", line 74, in run
essentiality_files = self.run_essentiality(plotfile_objects)
File "/home/amy/anaconda3/lib/python3.7/site-packages/albatradis/BlockInsertions.py", line 117, in run_essentiality
f = self.essentiality(plotfile_objects, plotfile, 'forward')
File "/home/amy/anaconda3/lib/python3.7/site-packages/albatradis/BlockInsertions.py", line 107, in essentiality
e.run()
File "/home/amy/anaconda3/lib/python3.7/site-packages/albatradis/TradisEssentiality.py", line 22, in run
subprocess.check_output(self.construct_command(), shell=True)
File "/home/amy/anaconda3/lib/python3.7/subprocess.py", line 395, in check_output
**kwargs).stdout
File "/home/amy/anaconda3/lib/python3.7/subprocess.py", line 487, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'tradis_essentiality.R /tmp/tmpyljazbl2' returned non-zero exit status 1.

Having issues with installation using conda. The edgeR/limma package that conda installs isn't correct or does not load properly, so the comparison module fails. Is there a way to update the dependencies that are installed to include a version of edgeR that works? Thanks so much :)

Hi,

Im having the issue with my output files, e.g combined.csv (generated with use_annotation) The first column of the file contains gene names rather than the locus tag and is therefore identical to column 2. Where no gene name has been allocated for gene in that particular genome the start and end position of the genes are listed in both columns (this can be quite a lot in less well characterised genomes). In the 3rd column it also doesn't seem to be pulling the info from the embl file and just lists "product" for every gene. Im not sure this is my embl file as it outputs correctly when running the biotradis tradis_comparison.R . Thanks for any suggestions you might have.

Hi,
When i run the albatradis with the -v option i get this at the end:
File "/home/ubuntu/anaconda2/envs/newenv/bin/albatradis", line 62, in
albatradis.run()
File "/home/ubuntu/anaconda2/envs/newenv/lib/python3.6/site-packages/albatradis/AlbaTraDIS.py", line 64, in run
self.cleanup()
File "/home/ubuntu/anaconda2/envs/newenv/lib/python3.6/site-packages/albatradis/AlbaTraDIS.py", line 79, in cleanup
print("Deleting file: "+ os.path.join(directory_to_search, filename) + " regex:"+deletion_regex)
NameError: name 'directory_to_search' is not defined

i still get all the output files plus some temp files.
Thanks

Hi,
is there a reason why a gene report.csv file would not be produced in the output folder. sometimes when i run albatradis it is produced and sometimes it isnt?

Thanks