Notice

The script runs on Linux system
Do not change and delete any files in AcrDetector

Requirement

HMMER 3.3
python 3.7
pandas
numpy
joblib
biopython
scikit-learn

Please install HMMER and add it to your PATH
Please install packages listed above before using this script

Running

if you have add the script to your PATH, you can run it like
python AcrDetector.py -i [or --infile] <infile> -o [or --output] <output>
if the script doesn't in PATH, run it using the path of AcrDetector.py plus
AcrDetector.py -i [or --infile] <infile> -o [or --output] <output>

-i or --infile: specify the input file
<infile>: file storing all CDS of whole genome in a fasta format. See the format in ./examples path
-o or --outfile: specify the output file
<output>: output filename

For example
python AcrDetector.py -i ./examples/GCF_001188875.1.fna -o re
This command means searching Acrs in GCF_001188875.1.fna and 
The results will be stored in re*

output

After running python AcrDetector.py -i ./examples/GCF_001188875.1.fna -o re
Four files prefixed with "re" are formed
    re, re_domain, re_protein and re_tbl
re: potential Acrs
re_domain and re_tbl: hth domain. hmmscan results in different formats
re_protein: translated protein from CDS region

There are 12 colums spaced by tab in re

Codirection
1: target gene and one of its neighbor gene are on the same strand
0: target gene and both of its neighbors aren't in the same strand

LNL: left neighbor length of target gene
TL: target gene length
RNL: right neighbor length of target gene

Function
    1: annotated as hypothetical protein, Uncharacterized protein, uncharacterized protein in NCBI
    0: annotated as validated function

codon distance: codon distance against whole genome
LDev: codon usage deviation of left neighbor gene compared with whole genome
TDev: codon usage deviation of target gene compared with whole genome
RDev: codon usage deviation of right neighbor gene compared with whole genome

HTH:
    "1": there is an HTH domain within 3 downstream genes of target gene based on the HTH Pfam_V32
    "0": No HTH domain within 3 downstream genes of target gene based on the HTH Pfam_V32

Score:
    Probability estimation

If you find bugs, please let me know chuand@whu.edu.cn