brandynwest
commented
4 years ago It seems like the problem might be with seaborn. The code in seaborn pallettes.py around line 777 is:
`colors = [_color_to_rgb(color, input) for color in colors] name = "blend" pal = mpl.colors.LinearSegmentedColormap.from_list(name, colors) if not as_cmap:
BW - original code: pal = _ColorPalette(pal(np.linspace(0, 1, n_colors)))
pal = _ColorPalette(pal(np.linspace(0, 1, int(n_colors))))
return pal'I was able to run abstar after using the int() function as shown in the code above.
briney
First off, abstar looks like a sweet program. Can't wait to give it a try. I found it while looking for an open source alternative to IMGT. This may be a problem with my installation, but I am getting an error when I try to run abstar from the command line. I updated both numpy and Matplotlib using pip and I am still getting the same error. I'm running python 3.8 on Mac OS Catalina. I get the same error from both terminal and Xquartz. Is this perhaps an issue with new versions of numpy?[https://github.com/pydata/numexpr/issues/354]
Here is a copy of the error as it is displayed in terminal:
`TestData brandyn$ abstar -i consensus_sequences.fasta -o abstarout/ Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/core/function_base.py", line 117, in linspace num = operator.index(num) TypeError: 'float' object cannot be interpreted as an integer
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.8/bin/abstar", line 29, in
import abstar
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/abstar/init.py", line 3, in
from .core.abstar import run, run_standalone, main, parse_arguments, validate_args
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/abstar/core/abstar.py", line 44, in
from abutils.core.sequence import Sequence
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/abutils/init.py", line 6, in
from .utils import alignment, cluster, decorators, jobs, log, phylogeny, pipeline, progbar, s3, utilities
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/abutils/utils/phylogeny.py", line 55, in
from .color import hex_to_rgb, get_cmap
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/abutils/utils/color.py", line 41, in
cmaps = {'heatmap': sns.diverging_palette(240, 10, as_cmap=True)}
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/seaborn/palettes.py", line 744, in diverging_palette
neg = palfunc((h_neg, s, l), 128 - (sep / 2), reverse=True, input="husl")
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/seaborn/palettes.py", line 641, in light_palette
return blend_palette(colors, n_colors, as_cmap)
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/seaborn/palettes.py", line 777, in blend_palette
pal = _ColorPalette(pal(np.linspace(0, 1, n_colors)))
File "<__array_function__ internals>", line 5, in linspace
File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/core/function_base.py", line 119, in linspace
raise TypeError(
TypeError: object of type <class 'float'> cannot be safely interpreted as an integer.`