Lenore Pipes

I am trying to print a sashimi plot but I always get hung up on this issue: File "/home/lp364/software/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_pdf.py", line 2078, in _get_font_ttf filename = findfont(prop) File "/home/lp364/software/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py", line 1418,...

setup.py

1

Hello, Is there a `setup.py` script so that I can install from source? Thank you.

Hi, I am trying to use the Needleman-Wunsch alignment part of your code in my program that is threaded. I am having issues parallelizing the code specifically around the function...

Hi, I am getting this error when I try to run pplacer. I think it has something to do with the tax table that taxtastic generated but I'm not sure....

No such file or directory: 'kmc'

1

``` saffrontree saffrontree_out Results/tree_estimation.fasta Traceback (most recent call last): File "/home/lenore/.local/bin/saffrontree", line 4, in __import__('pkg_resources').run_script('saffrontree==0.1.2', 'saffrontree') File "/home/lenore/.local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 662, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/lenore/.local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1466, in run_script...

masked alignment different from global tree in GISAID

5

Hello, I tried to download the masked alignment from GISAID but it contains >3 million sequences while the global tree they uploaded is only for ~600K sequences. Do you know...

I changed time timeout to 900 but it still doesn't work python3 gisaid-scrapper/scrap.py --filename credentials.txt --destination gisaid Traceback (most recent call last): File "gisaid-scrapper/scrap.py", line 55, in scrapper.login(login, passwd) File...