cnuge / alfie Goto Github PK

Hi,

I was working with COI sequences from EMBL and BOLD and was trying to filter out miss-assigned sequences. I merged both datasets, clustered at 99% and the used alfie to predict the taxonomy of the centroid sequence. In total it's 574135 sequences.

Here are my results for the agreement (in %) between the Kingdom given by BOLD / EMBL (harmonized with the GBIF backbone) and alfie predictions. I was wondering what you make of this? For Fungi, only 10 % of the sequences are classified?

Note that the classified bold sequences vary in length, I will update the results with consistent fragment lengths. Interestingly, the embl data are barcoding fragments (bc of the way I extracted them with ecopcr) while BOLD seqs are as found on BOLD and vary greatly in length.

Alfie is potentially super useful, so I don't mean to criticize in any way, just wondering what you though of the results below:

edit re-reading the preprint, I was wondering: How did you make sure the training data didn't contain miss-classifications? And if they did, would you expect that to have been a problem?

Hi,

I have reinstalled alfie on my new macbook pro

using either pip or downloading the github repo.

in either case alfie installs without problems but when I try to run it I get

macbook-pro:alfie-master fabian$ alfie
Illegal instruction: 4

Any idea what could be going on? This suggests it might me a TensorFlow Issue?

It appears that the manifest is missing at least one file necessary to build
from the sdist for version 1.0. You're in good company, about 5% of other
projects updated in the last year are also missing files.

+ /tmp/venv/bin/pip3 wheel --no-binary alfie -w /tmp/ext alfie==1.0
Looking in indexes: http://10.10.0.139:9191/root/pypi/+simple/
Collecting alfie==1.0
  Downloading http://10.10.0.139:9191/root/pypi/%2Bf/83b/7476586c67a28/alfie-1.0.tar.gz (40.2 MB)
    ERROR: Command errored out with exit status 1:
     command: /tmp/venv/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-z2f35r1_/alfie/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-z2f35r1_/alfie/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-wheel-z2f35r1_/alfie/pip-egg-info
         cwd: /tmp/pip-wheel-z2f35r1_/alfie/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-wheel-z2f35r1_/alfie/setup.py", line 3, in <module>
        with open('requirements.txt') as f:
    FileNotFoundError: [Errno 2] No such file or directory: 'requirements.txt'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.