Error in installation

[ofleitas]

Hello !!

I am trying to install antifungal but I got the follow error

Defaulting to user installation because normal site-packages is not writeable ERROR: Ignored the following versions that require a different python version: 0.1.0 Requires-Python >=3.6, <3.9; 0.1.2 Requires-Python <3.9,>=3.6; 0.1.3 Requires-Python <3.9,>=3.6 ERROR: Could not find a version that satisfies the requirement antifungal (from versions: none) ERROR: No matching distribution found for antifungal What can I do?

[JinZhangLab]

Hello !!

I am trying to install antifungal but I got the follow error

Defaulting to user installation because normal site-packages is not writeable ERROR: Ignored the following versions that require a different python version: 0.1.0 Requires-Python >=3.6, <3.9; 0.1.2 Requires-Python <3.9,>=3.6; 0.1.3 Requires-Python <3.9,>=3.6 ERROR: Could not find a version that satisfies the requirement antifungal (from versions: none) ERROR: No matching distribution found for antifungal What can I do?

It looks like you're encountering this issue because the antifungal package currently only supports Python versions 3.6 to 3.8, while your environment may be using a version outside this range (possibly Python 3.9 or higher). First, confirm which Python version you are using. You can do this by running:

python --version

If the version is 3.9 or higher, that's likely the reason for the incompatibility. You can create a virtual environment with Python 3.6, 3.7, or 3.8 to install antifungal. I recommend using conda to create a compatible virtual environment and then install with the following commands:

conda env create -n antifungal python=3.8
pip install antifungal

[ofleitas]

Thank you it worked.

I have a last question. My input is a txt file with lot of sequences. What can I do for the program read directly the sequences from the file without me having to manually enter them one by one?

[JinZhangLab]

To process multiple sequences from a text file for MIC prediction, you can read the sequences into a list and pass them directly to the predict_MIC function. If your input is in FASTA format, Biopython can be utilized to read the sequences efficiently.

For a plain text file with one sequence in one row (sequences.txt):

from antifungal.predict import predict_MIC

def read_sequences(file_path):
    with open(file_path, 'r') as f:
        sequences = [line.strip() for line in f if line.strip()]
    return sequences

seq = read_sequences('sequences.txt')
pred = predict_MIC(seq)
print(pred)

For a FASTA file (sequences.fasta):

from Bio import SeqIO
from antifungal.predict import predict_MIC

def read_fasta(file_path):
    sequences = [str(record.seq) for record in SeqIO.parse(file_path, 'fasta')]
    return sequences

seq = read_fasta('sequences.fasta')
pred = predict_MIC(seq)
print(pred)

Note: While MIC prediction supports batch processing of multiple sequences, rational design methods currently handle one sequence at a time.

[ofleitas]

Thank you very much.

I am trying to install antifungal in another pc, but I am getting the same initial error. I don't know why. I tried python=3.8 and 3.7 but didn't work for me.

(base) ofm@ofm:~$ conda activate antifungal (antifungal) ofm@ofm:~$ pip install antifungal Defaulting to user installation because normal site-packages is not writeable ERROR: Ignored the following versions that require a different python version: 0.1.0 Requires-Python >=3.6, <3.9; 0.1.2 Requires-Python <3.9,>=3.6; 0.1.3 Requires-Python <3.9,>=3.6 ERROR: Could not find a version that satisfies the requirement antifungal (from versions: none) ERROR: No matching distribution found for antifungal (antifungal) ofm@ofm:~$ python --version Python 3.7.16 (antifungal) ofm@ofm:~$

(base) ofm@ofm:~$ conda activate antifungal.1 (antifungal.1) ofm@ofm:~$ pip install antifungal Defaulting to user installation because normal site-packages is not writeable ERROR: Ignored the following versions that require a different python version: 0.1.0 Requires-Python >=3.6, <3.9; 0.1.2 Requires-Python <3.9,>=3.6; 0.1.3 Requires-Python <3.9,>=3.6 ERROR: Could not find a version that satisfies the requirement antifungal (from versions: none) ERROR: No matching distribution found for antifungal (antifungal.1) ofm@ofm:~$ python --version Python 3.8.20 (antifungal.1) ofm@ofm:~$