Replidec 0.3.5

Replication Cycle Decipher for Phages

Replidec: Replication Cycle Decipher for Phages

Aim

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

Install

Method 1: using Conda (Recommend using bioconda with latest version)

conda create -n replidec
conda activate replidec
conda install -c conda-forge -c bioconda replidec
or
conda install -c denglab -c conda-forge -c bioconda replidec

Method 2: using Docker

docker pull quay.io/biocontainers/replidec:0.3.4--pyhdfd78af_0 
docker run quay.io/biocontainers/replidec:0.3.4--pyhdfd78af_0 Replidec -h
## Example
docker run -v /your/host/data:/data/ quay.io/biocontainers/replidec:0.3.4--pyhdfd78af_0 Replidec -i data/your_inputfile -p multiSeqEachAsOne -w data

Method 3: using pip

If you install using pip, please make sure that mmseqs, hmmsearch and blastp is 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+

pip3 install Replidec

Usage: Overview

Replidec, Replication cycle prediction tool for prokaryotic viruses

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -p , --program        { multi_fasta | genome_table | protein_table }
                        
                        multi_fasta mode:
                        input is a fasta file and treat each sequence as one virus
                        
                        genome_table mode:
                        input is a tab separated file with two columns
                        ___1st column: sample name
                        ___2nd column: path to the genome sequence file of the virus
                        
                        protein_table mode:
                        input is a tab separated file with two columns
                        ___1st column: sample name
                        ___2nd column: path to the protein file of the virus
                        
  -i , --input_file     The input file, which can be a sequence file or an index table
  -w , --work_dir       Directory to store intermediate and final results (default = ./Replidec_results)
  -n , --file_name      Name of final summary file (default = prediction_summary.tsv)
  -t , --threads        Number of parallel threads (default = 10)
  -e , --hmmer_Eval     E-value threshold to filter hmmer result (default = 1e-5)
  -E , --hmmer_parameters 
                        Parameters used for hmmer (default = --noali --cpu 3)
  -m , --mmseq_Eval     E-value threshold to filter mmseqs2 result (default = 1e-5)
  -M , --mmseq_parameters 
                        Parameter used for mmseqs
                        (default = -s 7 --max-seqs 1 --alignment-mode 3 --alignment-output-mode 0 --min-aln-len 40 --cov-mode 0 --greedy-best-hits 1 --threads 3)
  -b , --blastp_Eval    E-value threshold to filter blast result (default =1e-5)
  -B , --blastp_parameter 
                        Parameters used for blastp (default = -num_threads 3)
  -d, --db_redownload   Remove and re-download database

Usage: Download database (-d)

Database used in Replidec will be download automatically.

Location: will be download at the where Replidec installed

If you want to redownload the database, -d parameter can be used. The older database will be mv to "discarded_db" in the workdir(-w); This dir can be removed manually by user.

Usage: Input (-i) and Propgram (-p)

Input file is different base on different program

Replidec cantain 3 different program:

1. 'multi_fasta'
2. 'genome_table'
3. 'protein_table',

multi_fasta mode:

• input is a fasta file and treat each sequence as one virus.

  • Example: <your_path>/viral_contigs.fasta

    >contig_1
    TATCGATCGATCGATCGATCGATCGTACGTACGTACGTACG...
    >contig_2
    CATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG...
    ...
    

genome_table mode:

• input is a tab separated file with two columns.

  • 1st column: sample name
  • 2nd column: path to the genome sequence file of the virus
  • Example: <your_path>/example_genomes.tsv

  contig_1    your/file/path/contig_1.fasta
  contig_2    your/file/path/contig_2.fasta
  contig_3    your/file/path/contig_3.fasta
  ...
  

protein_table mode:

• input is a tab separated file with two columns

  • 1st column: sample name
  • 2nd column: path to the protein file of the virus
  • Example: <your_path>/example_proteins.tsv

  contig_1_prot	your/file/path/contig_1.fasta
  contig_2_prot	your/file/path/contig_2.fasta
  contig_3_prot   your/file/path/contig_3.fasta
  ...
  

Usage: Output (-w and -n)

The output directory can be assigned with -w , --work_dir where the intermidiate files and the final prediction results will be stored. The name of the final summary file can be assigned with -n , --file_name argument.

At the end of the analysis, the output directory would contain the following:

• BC_Inno: This directory contains the result file for dectect Innovirues
• BC_mmseqs: This directory contains the result file for mapping result to our custom database
• BC_pfam: This directory contains the result file for dectect the Integrase and Excisionase
• BC_prodigal: This directory contains the result file for CDS prediction from genome or contig sequence. (if {-p protein_table} is used, this directory will not be created)
• prediction_summary.tsv: This file is the summary file of the predict result. It contain multiple coloumns.

  • sample_name: identifier. Can be sequence id or first coloumn the plain text input file.

  • integrase_number: the number of genes mapped to integrase meet the creteria(set by -c).

  • excisionase_number: the number of genes mapped to excisionase meet the creteria(set by -c).

  • pfam_label: if contain integrase or excisionase, label will be "Temperate". otherwise "Virulent".

  • bc_temperate: conditional probability of temperate|genes.

  • bc_virulent: conditional probability of virulent|genes.

  • bc_label: if bc_temperate greater than bc_virulent, label will be "Temperate". otherwise "Virulent".

  • final_label: if pfam_label and bc_label both is Temperate, then label will be "Temperate"; if Innovirues marker gene exist, then label will be "Chronic"; otherwise "Virulent".

  • match_gene_number: the number of genes mapped to our custom databse.

  • path: path of input faa file

Example

## test passed - multi_fasta mode
Replidec -p multi_fasta -i my/path/test_viral_contigs.fasta -w my/path/replidec_test_VC_results