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GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

License: Other

Python 99.53% Dockerfile 0.47%

bioinformatics-visualization genomics-visualization visualization-tools

genovi's People

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jiangchb cbuil sajjadasaf lipingshu parvathysuresh21 utguang pythseq anp16 erinchen6 090478

genovi's Issues

--title 'filename' does not work

SVGs and PNGs that are generated have "filename" in the center of the image.

Windows installation

I've run into an issue with installing circos on Windows 10 64-bit. It requires perl-clone but the conda package only supports linux-64 v0.46 and osx-64 v0.46. Has anyone installed GenoVi on Windows? Is there a work around to this issue?

problem with NCBI genebank files

I encountered the following error when running genovi with a genebank file downloaded from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/AL513382.1). I downloaded the files manually via send to > complete record > file > genebank as well as send to > complete record > file > genebank (full).
With both files I get:

$ genovi -i CT18_genebank_full.gb -o test -te -cs strong -s complete --size
/home/Uelze/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning
'locus_tag'
Error when transforming gbk to faa.
test-temp/contig_1-test_bands.kar created succesfully.
Traceback (most recent call last):
  File "/home/Uelze/miniconda3/envs/genovi/bin/genovi", line 8, in <module>
    sys.exit(main())
  File "/home/Uelze/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
    visualiseGenome(*get_args())
  File "/home/Uelze/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 341, in visualiseGenome
    sizes, cogs_p, cogs_n, lengths, chrms, hist, wanted_cogs = base(file, temp_folder + "/" + output_file_part, output_file + "/" + output_file, True, True, cogs_classified, cogs_classified, False, True, deepnog_confidence_threshold, verbose, wanted_cogs=wanted_cogs)
  File "/home/Uelze/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 499, in base
    _ , _, chrms_tp, chrms_tn, _ = create_feature(gbk_file, tmp, output, sizes, "tRNA", verbose = verbose, complete=complete)
  File "/home/Uelze/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 321, in create_feature
    locus_tag = feature.qualifiers.get("locus_tag")[0]
TypeError: 'NoneType' object is not subscriptable

I tried genovi with the test data of the github repository and it works just fine. I also found a workaround, by downloading the fasta file from NCBI, annotating it with bakta and then running genovi with the *.gbff file. This also works. So it seems to be a problem with the format of the NCBI genbank file?

jupyter notebook example?

Could you create a jupyter notebook example?

Issue with installing GenoVi

Hi!

I would like to use GenoVi to visualize some of my genomes, but I've ran into an error in the installing process. It seems that the matplotlib version 3.5.2 isn't available for some reason. What could be the reason and how could I solve it?

pip3 install genovi
Collecting genovi
Using cached https://files.pythonhosted.org/packages/b2/20/e6517ede1396e1bd0754b8ec76e4d9f6d555d036cff650ccf0c506f7aeb6/genovi-0.4.3.tar.gz
Collecting cairosvg>=2.5.2 (from genovi)
Using cached https://files.pythonhosted.org/packages/01/a5/1866b42151f50453f1a0d28fc4c39f5be5f412a2e914f33449c42daafdf1/CairoSVG-2.7.1-py3-none-any.whl
Collecting matplotlib>=3.5.2 (from genovi)
Could not find a version that satisfies the requirement matplotlib>=3.5.2 (from genovi) (from versions: 0.86, 0.86.1, 0.86.2, 0.91.0, 0.91.1, 1.0.1, 1.1.0, 1.1.1, 1.2.0, 1.2.1, 1.3.0, 1.3.1, 1.4.0, 1.4.1rc1, 1.4.1, 1.4.2, 1.4.3, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 2.0.0b1, 2.0.0b2, 2.0.0b3, 2.0.0b4, 2.0.0rc1, 2.0.0rc2, 2.0.0, 2.0.1, 2.0.2, 2.1.0rc1, 2.1.0, 2.1.1, 2.1.2, 2.2.0rc1, 2.2.0, 2.2.2, 2.2.3, 2.2.4, 2.2.5, 3.0.0rc2, 3.0.0, 3.0.1, 3.0.2, 3.0.3, 3.1.0rc1, 3.1.0rc2, 3.1.0, 3.1.1, 3.1.2, 3.1.3, 3.2.0rc1, 3.2.0rc3, 3.2.0, 3.2.1, 3.2.2, 3.3.0rc1, 3.3.0, 3.3.1, 3.3.2, 3.3.3, 3.3.4)
No matching distribution found for matplotlib>=3.5.2 (from genovi)

Output colours used for COGs in plots and legends do not match

While the colours for the legends for Genomic Features match those shown in genome plots, those for the COGs do not. E.g. #909090 used for COG category S on plot, but #999999 used in legend; #626262 used for COG category R on plot, but #696969 in legend. I only noticed this when I tried searching for same colours across the genovi outputs in Illustrator. Not a huge issue as you have made it possible to run genovi with specific COG outputs, but means that if I and others want to highlight specific aspects of complex plots there's no way we can match/find COG categories in the images.

Docker availability

Hi, the paper mentioned a docker container is available for GenoVi.
How can I pull it?
can't find the relevant image online

GenoVi does not scale well

When processing a directory of GBFFs, GenoVi does this in serial instead of parallel fashion. Attempting to work around this by 'parallelizing' the workflow using GNU parallel also unfortunately results in path-related errors, and then we also lose the summary data (such as the scaled joined figure of all the circular representations and output tables summarizing the general statistics) that operating in 'directory mode' gives us. It wouldn't be hard to build this into GenoVi using the futures or multiprocessing modules.

Drawing error

Hi,
I am unable to get the diagram with the following error. The input file used is GBK format.
I believe the software has been successfully installed.

$ genovi -i annotation.gbk -s complete -cs paradice -bc white
/home/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning

GBK file transformed into faa succesfully. File saved as genovi-temp/contig_1-genovi.faa
output genovi-temp/contig_1-genovi

Deepnog prediction started

deepnog infer genovi-temp/contig_1-genovi.faa --out genovi-temp/contig_1-genovi_prediction_deepnog.csv -db cog2020 -t 1
[2023-08-02 09:02:14] deepnog.client.client - INFO - Starting deepnog
[2023-08-02 09:03:21] deepnog.client.client - INFO - Loading NN-parameters from /home/deepnog_data/cog2020/1/deepnog.pth ...
[2023-08-02 09:03:21] deepnog.client.client - INFO - Accessing dataset from genovi-temp/contig_1-genovi.faa ...
[2023-08-02 09:03:22] deepnog.client.client - INFO - Starting protein sequence group/family inference ...
[2023-08-02 09:03:22] deepnog.learning.inference - INFO - Inference device: cpu
deepnog inference: 2.46kseq [00:45, 53.5seq/s]
[2023-08-02 09:04:08] deepnog.learning.inference - INFO - Inference complete.
[2023-08-02 09:04:09] deepnog.client.client - INFO - Writing prediction to genovi-temp/contig_1-genovi_prediction_deepnog.csv
[2023-08-02 09:04:09] deepnog.client.client - INFO - All done.

Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_1-genovi_prediction_deepnog.csv

/home/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning
genovi-temp/contig_1-genovi_bands.kar created succesfully.
genovi-temp/contig_1-genovi_tRNA_pos.txt created succesfully.
.
.
.
Transforming GenBank record sequence1.1 to .fna
Done
Drawing 1...
Traceback (most recent call last):
  File "/home/miniconda3/envs/genovi/bin/genovi", line 8, in <module>
    sys.exit(main())
  File "/home/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
    visualiseGenome(*get_args())
  File "/home/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 382, in visualiseGenome
    os.rename("circos.svg", output_file + "-contig_" + str(i) + ".svg")
FileNotFoundError: [Errno 2] No such file or directory: 'circos.svg' -> 'genovi-contig_1.svg'

Thanks

Tutorial fails

I followed the installation instructions (used conda to install python and circos and then pip to install the latest version of GenoVi - which is 0.4.3).

I have been following the tutorial and ran into this issue

$ genovi -i input_test/Acinetobacter_radioresistens_DD78.gbff -cs strong -s complete --size                                                   
#0 4.922 [2023-11-08 21:07:23] deepnog.client.client - INFO - Starting deepnog                                                                                                     
#0 7.993 [2023-11-08 21:07:26] deepnog.client.client - INFO - Loading NN-parameters from /root/deepnog_data/cog2020/1/deepnog.pth ...                                              
#0 8.012 [2023-11-08 21:07:26] deepnog.client.client - INFO - Accessing dataset from genovi-temp/contig_1-genovi.faa ...                                                           
#0 8.069 [2023-11-08 21:07:26] deepnog.client.client - INFO - Starting protein sequence group/family inference ...                                                                 
#0 8.069 [2023-11-08 21:07:26] deepnog.learning.inference - INFO - Inference device: cpu
deepnog inference: 2.67kseq [00:42, 62.7seq/s]
#0 50.67 [2023-11-08 21:08:09] deepnog.learning.inference - INFO - Inference complete.
#0 50.68 [2023-11-08 21:08:09] deepnog.client.client - INFO - Writing prediction to genovi-temp/contig_1-genovi_prediction_deepnog.csv
#0 50.69 [2023-11-08 21:08:09] deepnog.client.client - INFO - All done.
#0 75.95 [2023-11-08 21:08:34] deepnog.client.client - INFO - Starting deepnog
#0 76.39 [2023-11-08 21:08:34] deepnog.client.client - INFO - Loading NN-parameters from /root/deepnog_data/cog2020/1/deepnog.pth ...
#0 76.41 [2023-11-08 21:08:34] deepnog.client.client - INFO - Accessing dataset from genovi-temp/contig_2-genovi.faa ...
#0 76.47 [2023-11-08 21:08:35] deepnog.client.client - INFO - Starting protein sequence group/family inference ...
#0 76.47 [2023-11-08 21:08:35] deepnog.learning.inference - INFO - Inference device: cpu
deepnog inference: 68.0seq [00:01, 59.0seq/s]
#0 77.62 [2023-11-08 21:08:36] deepnog.learning.inference - INFO - Inference complete.
#0 77.63 [2023-11-08 21:08:36] deepnog.client.client - INFO - Writing prediction to genovi-temp/contig_2-genovi_prediction_deepnog.csv
#0 77.63 [2023-11-08 21:08:36] deepnog.client.client - INFO - All done.
#0 83.83 [2023-11-08 21:08:42] deepnog.client.client - INFO - Starting deepnog
#0 84.23 [2023-11-08 21:08:42] deepnog.client.client - INFO - Loading NN-parameters from /root/deepnog_data/cog2020/1/deepnog.pth ...
#0 84.24 [2023-11-08 21:08:42] deepnog.client.client - INFO - Accessing dataset from genovi-temp/contig_3-genovi.faa ...
#0 84.30 [2023-11-08 21:08:42] deepnog.client.client - INFO - Starting protein sequence group/family inference ...
#0 84.30 [2023-11-08 21:08:42] deepnog.learning.inference - INFO - Inference device: cpu
deepnog inference: 71.0seq [00:00, 113seq/s]
#0 84.93 [2023-11-08 21:08:43] deepnog.learning.inference - INFO - Inference complete.
#0 84.93 [2023-11-08 21:08:43] deepnog.client.client - INFO - Writing prediction to genovi-temp/contig_3-genovi_prediction_deepnog.csv
#0 84.94 [2023-11-08 21:08:43] deepnog.client.client - INFO - All done.
#0 85.57 There's been an error finding cairoSVG library, so PNG images might be different from expected. Please prefer using SVG output.
#0 85.57 
#0 85.57 GBK file transformed into faa succesfully. File saved as genovi-temp/contig_1-genovi.faa
#0 85.57 output genovi-temp/contig_1-genovi
#0 85.57 
#0 85.57 Deepnog prediction started
#0 85.57 
#0 85.57 deepnog infer genovi-temp/contig_1-genovi.faa --out genovi-temp/contig_1-genovi_prediction_deepnog.csv -db cog2020 -t 1
#0 85.57 
#0 85.57 Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_1-genovi_prediction_deepnog.csv
#0 85.57 
#0 85.57 genovi-temp/contig_1-genovi_bands.kar created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_tRNA_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_tRNA_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_rRNA_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_rRNA_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_C.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_D.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_E.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_F.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_G.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_H.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_I.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_J.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_K.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_L.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_M.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_N.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_O.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_P.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_Q.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_R.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_S.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_T.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_U.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_V.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_W.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_X.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos_None.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_A.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_C.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_D.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_E.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_F.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_G.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_H.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_I.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_J.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_K.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_L.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_M.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_N.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_O.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_P.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_Q.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_R.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_S.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_T.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_U.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_V.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_X.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg_None.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_1-genovi_CDS_neg.txt created succesfully.
#0 85.57 Transforming GenBank record CP038022.1 to .fna
#0 85.57 Done
#0 85.57 Drawing 1...
#0 85.57 
#0 85.57 GBK file transformed into faa succesfully. File saved as genovi-temp/contig_2-genovi.faa
#0 85.57 output genovi-temp/contig_2-genovi
#0 85.57 
#0 85.57 Deepnog prediction started
#0 85.57 
#0 85.57 deepnog infer genovi-temp/contig_2-genovi.faa --out genovi-temp/contig_2-genovi_prediction_deepnog.csv -db cog2020 -t 1
#0 85.57 
#0 85.57 Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_2-genovi_prediction_deepnog.csv
#0 85.57 
#0 85.57 genovi-temp/contig_2-genovi_bands.kar created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_tRNA_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_tRNA_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_rRNA_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_rRNA_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_C.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_E.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_G.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_I.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_K.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_M.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_N.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_O.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_P.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_R.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_T.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_V.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_X.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos_None.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_C.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_D.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_H.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_I.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_K.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_L.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_M.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_N.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_O.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_P.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_R.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_V.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_X.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg_None.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_2-genovi_CDS_neg.txt created succesfully.
#0 85.57 Transforming GenBank record CP038023.1 to .fna
#0 85.57 Done
#0 85.57 Drawing 2...
#0 85.57 
#0 85.57 GBK file transformed into faa succesfully. File saved as genovi-temp/contig_3-genovi.faa
#0 85.57 output genovi-temp/contig_3-genovi
#0 85.57 
#0 85.57 Deepnog prediction started
#0 85.57 
#0 85.57 deepnog infer genovi-temp/contig_3-genovi.faa --out genovi-temp/contig_3-genovi_prediction_deepnog.csv -db cog2020 -t 1
#0 85.57 
#0 85.57 Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_3-genovi_prediction_deepnog.csv
#0 85.57 
#0 85.57 genovi-temp/contig_3-genovi_bands.kar created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_tRNA_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_tRNA_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_rRNA_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_rRNA_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_neg.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_C.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_D.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_F.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_I.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_J.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_K.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_L.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_O.txt created succesfully.
#0 85.57 genovi-temp/contig_3-genovi_CDS_pos_R.txt created succesfully.[2023-11-08 21:08:49] deepnog.client.client - INFO - Starting deepnog
#0 91.67 [2023-11-08 21:08:50] deepnog.client.client - INFO - Loading NN-parameters from /root/deepnog_data/cog2020/1/deepnog.pth ...
#0 91.69 [2023-11-08 21:08:50] deepnog.client.client - INFO - Accessing dataset from genovi-temp/contig_4-genovi.faa ...
#0 91.74 [2023-11-08 21:08:50] deepnog.client.client - INFO - Starting protein sequence group/family inference ...
#0 91.74 [2023-11-08 21:08:50] deepnog.learning.inference - INFO - Inference device: cpu
deepnog inference: 70.0seq [00:01, 57.9seq/s]
#0 92.95 [2023-11-08 21:08:51] deepnog.learning.inference - INFO - Inference complete.
#0 92.95 [2023-11-08 21:08:51] deepnog.client.client - INFO - Writing prediction to genovi-temp/contig_4-genovi_prediction_deepnog.csv
#0 92.96 [2023-11-08 21:08:51] deepnog.client.client - INFO - All done.
#0 99.08 /usr/local/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
#0 99.08   "Premature end of file in sequence data", BiopythonParserWarning
#0 99.08 /usr/local/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
#0 99.08   "Premature end of file in sequence data", BiopythonParserWarning
#0 99.08 /usr/local/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
#0 99.08   "Premature end of file in sequence data", BiopythonParserWarning
#0 99.08 /usr/local/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
#0 99.08   "Premature end of file in sequence data", BiopythonParserWarning
#0 99.08 /usr/local/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
#0 99.08   "Premature end of file in sequence data", BiopythonParserWarning
#0 99.08 
#0 99.08 genovi-temp/contig_3-genovi_CDS_pos_S.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_pos_T.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_pos_U.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_pos_V.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_pos_X.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_pos_None.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_C.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_D.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_E.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_G.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_J.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_K.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_L.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_M.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_N.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_O.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_P.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_Q.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_R.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_T.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_U.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_V.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_X.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg_None.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_pos.txt created succesfully.
#0 99.08 genovi-temp/contig_3-genovi_CDS_neg.txt created succesfully.
#0 99.08 Transforming GenBank record CP038024.1 to .fna
#0 99.08 Done
#0 99.08 Drawing 3...
#0 99.08 
#0 99.08 GBK file transformed into faa succesfully. File saved as genovi-temp/contig_4-genovi.faa
#0 99.08 output genovi-temp/contig_4-genovi
#0 99.08 
#0 99.08 Deepnog prediction started
#0 99.08 
#0 99.08 deepnog infer genovi-temp/contig_4-genovi.faa --out genovi-temp/contig_4-genovi_prediction_deepnog.csv -db cog2020 -t 1
#0 99.08 
#0 99.08 Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_4-genovi_prediction_deepnog.csv
#0 99.08 
#0 99.08 genovi-temp/contig_4-genovi_bands.kar created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_tRNA_pos.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_tRNA_neg.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_rRNA_pos.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_rRNA_neg.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_C.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_D.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_H.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_I.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_J.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_K.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_L.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_M.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_O.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_P.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_Q.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_R.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_V.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_X.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos_None.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_C.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_H.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_I.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_J.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_K.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_L.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_M.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_O.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_P.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_Q.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_R.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_S.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_T.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_V.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_X.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg_None.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_pos.txt created succesfully.
#0 99.08 genovi-temp/contig_4-genovi_CDS_neg.txt created succesfully.
#0 99.08 Transforming GenBank record CP038025.1 to .fna
#0 99.08 Done
#0 99.08 Drawing 4...
#0 99.08 Traceback (most recent call last):
#0 99.08   File "/usr/local/bin/genovi", line 8, in <module>
#0 99.08     sys.exit(main())
#0 99.08   File "/usr/local/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
#0 99.08     visualiseGenome(*get_args())
#0 99.08   File "/usr/local/lib/python3.7/site-packages/scripts/GenoVi.py", line 421, in visualiseGenome
#0 99.08     os.rename(output_file + "-contig_" + str(i) + ".png", output_file + "/" + output_file + "-contig_" + str(i) + ".png")
#0 99.08 FileNotFoundError: [Errno 2] No such file or directory: 'genovi-contig_1.png' -> 'genovi/genovi-contig_1.png'

Font size changes?

Hi, is it possible to change font sizes? for the title, for the size, for the size on the circle, and for the key.

cheers

Issues with DeepNOG file not found + PNG

Hello!

I keep getting this error when trying to run my genome:

There's been an error finding cairoSVG library, so PNG images might be different from expected. Please prefer using SVG output.
/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning

GBK file transformed into faa succesfully. File saved as genovi-temp/contig_1-genovi.faa
output genovi-temp/contig_1-genovi

Deepnog prediction started

deepnog infer genovi-temp/contig_1-genovi.faa --out genovi-temp/contig_1-genovi_prediction_deepnog.csv -db cog2020 -t 1
[2023-10-08 19:08:43] deepnog.client.client - INFO - Starting deepnog
[2023-10-08 19:08:44] deepnog.client.client - INFO - Loading NN-parameters from /home/siljavah/deepnog_data/cog2020/1/deepnog.pth ...
Traceback (most recent call last):
  File "/home/siljavah/miniconda3/envs/genovi/bin/deepnog", line 8, in <module>
    sys.exit(main())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 481, in main
    _start_prediction_or_training(args)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 295, in _start_prediction_or_training
    return _start_inference(args=args, arch_module=module, arch_cls=cls)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 324, in _start_inference
    model_dict = torch.load(weights_path, map_location=args.device)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/torch/serialization.py", line 777, in load
    with _open_zipfile_reader(opened_file) as opened_zipfile:
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/torch/serialization.py", line 282, in __init__
    super(_open_zipfile_reader, self).__init__(torch._C.PyTorchFileReader(name_or_buffer))
RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory

Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_1-genovi_prediction_deepnog.csv

Traceback (most recent call last):
  File "/home/siljavah/miniconda3/envs/genovi/bin/genovi", line 8, in <module>
    sys.exit(main())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
    visualiseGenome(*get_args())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 341, in visualiseGenome
    sizes, cogs_p, cogs_n, lengths, chrms, hist, wanted_cogs = base(file, temp_folder + "/" + output_file_part, output_file + "/" + output_file, True, True, cogs_classified, cogs_classified, False, True, deepnog_confidence_threshold, verbose, wanted_cogs=wanted_cogs)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 482, in base
    cogs_dict = get_categories(gbk_file, tmp, deepnog_confidence)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 445, in get_categories
    cogs_df = pd.read_csv(output_pred, sep=',', usecols=['sequence_id', 'prediction'])
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper
    return func(*args, **kwargs)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 482, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 811, in __init__
    self._engine = self._make_engine(self.engine)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
    return mapping[engine](self.f, **self.options)  # type: ignore[call-arg]
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in __init__
    self._open_handles(src, kwds)
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/base_parser.py", line 229, in _open_handles
    errors=kwds.get("encoding_errors", "strict"),
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/common.py", line 707, in get_handle
    newline="",
FileNotFoundError: [Errno 2] No such file or directory: 'genovi-temp/contig_1-genovi_prediction_deepnog.csv'

I can get a PNG file if using -cu, but even then I get this error:

There's been an error finding cairoSVG library, so PNG images might be different from expected. Please prefer using SVG output.
/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning
genovi-temp/contig_1-genovi_bands.kar created succesfully.
genovi-temp/contig_1-genovi_tRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_tRNA_neg.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_neg.txt created succesfully.
genovi-temp/contig_1-genovi_CDS_pos.txt created succesfully.
genovi-temp/contig_1-genovi_CDS_neg.txt created succesfully.
Transforming GenBank record tig00000001 to .fna
Done
Drawing 1...
Traceback (most recent call last):
  File "/home/siljavah/miniconda3/envs/genovi/bin/genovi", line 8, in <module>
    sys.exit(main())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
    visualiseGenome(*get_args())
  File "/home/siljavah/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 421, in visualiseGenome
    os.rename(output_file + "-contig_" + str(i) + ".png", output_file + "/" + output_file + "-contig_" + str(i) + ".png")
FileNotFoundError: [Errno 2] No such file or directory: 'genovi-contig_1.png' -> 'genovi/genovi-contig_1.png'

Is there any way I could fix this? Just to note, I am just an undergraduate trying to do my bioinformatics project so if I've just done something very obviously wrong then please bare with me!

Annotating/labelling genes

Hi,

I've been using your tool for some time now to generate overviews of different genomes. I was wondering if there's a possibility to add custom labels/annotations to specific genes of interest?

For example to generate the GenoVi figure, but also label specific genes based on their locus/position?

Thanks in advance for answering the question, I love the tool and the work you have put into making it work smoothly! :)

Python errors in running GenoVi

Hi,

I was hoping to try out GenoVi to visualise a few of my genomes, but have run into an issue I was hoping you could help me with.

From what I can tell there seem to be two different issues, one is something related to the cairoSVG library, which doesn't seem to be a major issue, whereas the other one actually stops the run and seems to be related to with the GenoVi python script itself. Here's the command I submitted and the output:

$ genovi -i PROKKA_02082023.gbk -cs paradise -s complete --size --cogs_unclassified --title 'M30B9 sp.' --title_position top --italic_words 1 -te

There's been an error finding cairoSVG library, so PNG images might be different from expected. Please prefer using SVG output.
/Users/iwilkie/opt/anaconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
  "Premature end of file in sequence data", BiopythonParserWarning
genovi-temp/contig_1-genovi_bands.kar created succesfully.
genovi-temp/contig_1-genovi_tRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_tRNA_neg.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_pos.txt created succesfully.
genovi-temp/contig_1-genovi_rRNA_neg.txt created succesfully.
genovi-temp/contig_1-genovi_CDS_pos.txt created succesfully.
genovi-temp/contig_1-genovi_CDS_neg.txt created succesfully.
Transforming GenBank record LBDLHKHK_1 to .fna
Done
Drawing 1...
Traceback (most recent call last):
  File "/Users/iwilkie/opt/anaconda3/envs/genovi/bin/genovi", line 8, in <module>
    sys.exit(main())
  File "/Users/iwilkie/opt/anaconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
    visualiseGenome(*get_args())
  File "/Users/iwilkie/opt/anaconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 414, in visualiseGenome
    pCDS_colour = CDS_positive, nCDS_colour = CDS_negative, tRNA_colour = tRNA, rRNA_colour = rRNA, GC_content_colour = GC_content, font_colour = font_colour)
  File "/Users/iwilkie/opt/anaconda3/envs/genovi/lib/python3.7/site-packages/scripts/addText.py", line 52, in addText
    source = open(inFile)
FileNotFoundError: [Errno 2] No such file or directory: 'genovi/genovi.svg'

Would you happen to have any recommendations for how to fix/avoid this issue, and how to go forward?

I really appreciate any help you can provide, thanks in advance!

labeling

How to label the diagram using gene or protein ids

--output_file does not work properly

Specifying an output directory with a relative path causes errors, e.g. this fails:

$ mkdir genovi
$ genovi -o genovi/blah ...

Parsing path input with Pathlib Path(args.outfile).absolute() or os.path.abspath(args.outfile) would fix this.

Error at the DeepNOG step likely related to PyTorch

Hi,

I'm trying running GenoVi with a genbank file downloaded from GenBank.

But, I'm encountering an error at the DeepNOG step. Below is the stdout.
I can get plots successfully with "-cu" option.

How can I avoid this error?

-----
(genovi) kangin@user[xxx] genovi -i sequence.gb -s complete
/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/Bio/GenBank/Scanner.py:1219: BiopythonParserWarning: Premature end of file in sequence data
"Premature end of file in sequence data", BiopythonParserWarning

GBK file transformed into faa succesfully. File saved as genovi-temp/contig_1-genovi.faa
output genovi-temp/contig_1-genovi

Deepnog prediction started

deepnog infer genovi-temp/contig_1-genovi.faa --out genovi-temp/contig_1-genovi_prediction_deepnog.csv -db cog2020 -t 1
[2023-04-06 10:57:36] deepnog.client.client - INFO - Starting deepnog
[2023-04-06 10:57:37] deepnog.client.client - INFO - Loading NN-parameters from /home/kangin/deepnog_data/cog2020/1/deepnog.pth ...
Traceback (most recent call last):
File "/home/kangin/miniconda3/envs/genovi/bin/deepnog", line 8, in
sys.exit(main())
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 481, in main
_start_prediction_or_training(args)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 295, in _start_prediction_or_training
return _start_inference(args=args, arch_module=module, arch_cls=cls)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/deepnog/client/client.py", line 324, in _start_inference
model_dict = torch.load(weights_path, map_location=args.device)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/torch/serialization.py", line 777, in load
with _open_zipfile_reader(opened_file) as opened_zipfile:
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/torch/serialization.py", line 282, in init
super(_open_zipfile_reader, self).init(torch._C.PyTorchFileReader(name_or_buffer))
RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory

Deepnog prediction finished succesfully. Predictions saved as genovi-temp/contig_1-genovi_prediction_deepnog.csv

Traceback (most recent call last):
File "/home/kangin/miniconda3/envs/genovi/bin/genovi", line 8, in
sys.exit(main())
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 685, in main
visualiseGenome(*get_args())
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/GenoVi.py", line 341, in visualiseGenome
sizes, cogs_p, cogs_n, lengths, chrms, hist, wanted_cogs = base(file, temp_folder + "/" + output_file_part, output_file + "/" + output_file, True, True, cogs_classified, cogs_classified, False, True, deepnog_confidence_threshold, verbose, wanted_cogs=wanted_cogs)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 482, in base
cogs_dict = get_categories(gbk_file, tmp, deepnog_confidence)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/scripts/create_raw.py", line 445, in get_categories
cogs_df = pd.read_csv(output_pred, sep=',', usecols=['sequence_id', 'prediction'])
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 482, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 811, in init
self._engine = self._make_engine(self.engine)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
return mapping[engine](self.f, **self.options) # type: ignore[call-arg]
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in init
self._open_handles(src, kwds)
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/parsers/base_parser.py", line 229, in _open_handles
errors=kwds.get("encoding_errors", "strict"),
File "/home/kangin/miniconda3/envs/genovi/lib/python3.7/site-packages/pandas/io/common.py", line 707, in get_handle
newline="",
FileNotFoundError: [Errno 2] No such file or directory: 'genovi-temp/contig_1-genovi_prediction_deepnog.csv'
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