Replidec: Replication Cycle Decipher for Phages

Aim

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

Install

Method 1: using Conda

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 denglab/replidec

If you want to use Replidec on an HPC, singularity is recommended. You can create a singularity image using following command,

singularity pull replidec.sif docker://denglab/replidec

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 [-h] [--version] -p {multiSeqAsOne,batch,multiSeqEachAsOne}
         [-i INPUT_FILE] [-w WORKDIR] [-s SUMMARY] [-t THREADS] [-c HMMER_CRETERIA] [-H HMMER_PARAMETER] [-m MMSEQS_CRETERIA]
         [-M MMSEQS_PARAMETER] [-b BLASTP_CRETERIA] [-B BLASTP_PARAMETER] [-d] [-D]

Usage: database (-d & -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.

We provide 2 database for user choose. Use -D to choose database. all|prokaryote

1. all: This database contain all proteins from the prokaryotic, eukaryotic virus and prophage.
2. prokaryote: This database contain proteins from the prokaryotic virus and prophage. eukaryotic virus gene was removed from this database

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

Input file is different base on different program

Replidec cantain 3 different program:

1. 'multiSeqAsOne'
2. 'batch'
3. 'multiSeqEachAsOne',

multiSeqAsOne

• multiSeqAsOne mode: input is a plain text file contain two coloumn (seprator must be tab)

  • first column: sample name; this will be used as identfier in the output summary file

  • second column: path of the genome or contig file from one virues (Each file can contain multi seq)

  • Example: test/example/genome_test.small.index

  seq1    example/genome_test/genome.test.fnaaa
  seq2    example/genome_test/genome.test.fnaab
  seq3    example/genome_test/genome.test.fnaac
  

multiSeqEachAsOne

• multiSeqEachAsOne mode: input is a sequence file and treat each seqence as from one virus and give each sequence a predict result;

  • This mode will treat each sequence independently

  • Example: test/example/test.contig.small.fa

batch

• batch mode: input is a plain text file contain two coloumn (seprator must be tab);

  • first column: sample name;

  • second column: path of the protein file from one virues;

  • Example: test/example/example.small.list

  simulate_art_sample1.10 example/simulate_art_sample1.10.faa
  simulate_art_sample1.11 example/simulate_art_sample1.11.faa
  simulate_art_sample1.12 example/simulate_art_sample1.12.faa
  

Usage: Output(-w and -s)

The output dirname can use -w to set and the name of summary file can use -s to set. Under output dir serveral dir and a summary file will be generated

• BC_Inno: This dir contain the result file for dectect Innovirues
• BC_mmseqs: This dir contain the result file for mapping result to our custom database
• BC_pfam: This dir contain the result file for dectect the Integrase and Excisionase
• BC_prodigal: This dir contain the result file for CDS prediction from genome or contig sequence. (-p batch will not generate this dir)
• BC_predict.summary: 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 - multiSeqAsOne
Replidec -p multiSeqAsOne -i example/genome_test.small.index -w multiSeqAsOne

## test passed - multiSeqEachAsOne
Replidec -p multiSeqEachAsOne -i example/test.contig.small.fa -w multiSeqEachAsOne

## test passed - batch
Replidec -p batch -i example/example.small.list -w batch