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TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
http://www.earlham.ac.uk/kat-tools
GNU General Public License v3.0
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distanalysis.py plotting broken #104

Open duceppemo opened 6 years ago

duceppemo commented 6 years ago

I installed the KAT v2.4.1 through conda. Works like a charm, except the distanalysis.py script. The plotting function just fail to produce outputs. Looking at the code I found that it's because "args.format" never gets passed to the plotting function although it wants it. As a result, there is no output file names generated and no file to write too.

I hacked the code to remove any reference to "format" and hard coded "png" instead because that's what I wanted. Anyhow, I attached my working version of the script for reference.

distanalysis.py.zip

maplesond commented 6 years ago

Thanks for the feedback @duceppemo. I'll take a look at the changes you've made later in the week.

duceppemo commented 6 years ago

No problem. Like I said, the attached script is more to locate the places that need to be changed. I didn’t fixed it properly. I think it’s just a matter of passing the arg.format to the functions.

DomeJoyce commented 5 years ago

I install via source KAT v.2.4.2. Running kat_distanalysis --plot pe_vs_assembly-main.mx it fails to produce the plot with the following message: `Creating plots

Plotting K-mer frequency distributions for general spectra ... /home/joyce/.local/lib/python3.6/site-packages/matplotlib/figure.py:445: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure. % get_backend()) done. Plotting K-mer frequency distributions for 0x ... done. Plotting K-mer frequency distributions for 1x ... done. Plotting K-mer frequency distributions for 2x ... done. Plotting K-mer frequency distributions for 3x ... done. ` Did you have any solution to fix it?

Many thanks