Replidec 0.2.1

Replication Cycle Detector for Phages

Replidec: Replication Cycle Detector for Phages

Aim

Use bayes classifier combine with homology search to predict virus replication cycle

Important:

mmseqs, hmmsearch, blastp must set to $PATH, these software can equal or higher than version list below

MMseqs2 Version: 13.45111

HMMER 3.3.2 (Nov 2020)

Protein-Protein BLAST 2.5.0+

conda create -n replidec
conda activate replidec
conda install -c bioconda,anaconda "python>=3.8" mmseqs2 hmmer blast

Usage

add the destination dir(where you clone the tool) in your path

import sys
sys.path.append("your_path/bayes_classifier")

Example

from lifestyleBC import bayes_classifier_single,bayes_classifier_batch

for singe predict

bayes_classifier_single("./example/simulate_art_sample1.5.faa","simulate_art_sample1.5","./test")

output --> list

[prefix, inte_label, excision_label, pfam_label, p_total_temperate, p_total_lytic, bc_label, final_label]

for batch predict

bayes_classifier_batch("./example/example.list","./batch_test","BC_predict.summary")

output --> file same column like above