error with plot_cladogram.py about lefse HOT 3 CLOSED

Hi @fbeghini,

Thanks for your reply. I found another error:

Traceback (most recent call last):
  File "../plot_cladogram.py", line 340, in <module>
    clad_tree = read_data(params['input_file'],params)    
  File "../plot_cladogram.py", line 106, in read_data
    abundances = [float(v) for v in list(zip(*rows))[1] if v >= 0.0]
  File "../plot_cladogram.py", line 106, in <listcomp>
    abundances = [float(v) for v in list(zip(*rows))[1] if v >= 0.0]
TypeError: '>=' not supported between instances of 'str' and 'float'

I fixed it with abundances = [float(v) for v in list(zip(*rows))[1] if float(v) >= 0.0].

I forgot to say that I followed the bioconda-lefse_run.sh script in the example folder to run the tests. The link there also needs a fix.

I appreciate your time,
Best regards.

from lefse.

BTW, the full command was plot_cladogram.py hmp_aerobiosis_small.res hmp_aerobiosis_small.cladogram.png --format png

from lefse.

Hi Rodrigo, yes, thank you for spotting this, we have forgot to unlist the zip content when porting to Python 3.
This have been fixed in commit 4eb6faa

I also fixed the broken link in the LEfSE tutorial on bioBakery (hmp_small_aerobiosis.txt)

Best

from lefse.