Replidec 0.2.0

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

Install

pip3 install Replidec

Usage

Replidec [para]

Replidec cantain 6 different program: 'multiSeqAsOne','batch','multiSeqEachAsOne','test_multiSeqAsOne','test_batch','test_multiSeqEachAsOne'

• multiSeqAsOne 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

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

• 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;

• test_* mode: test for each prpgram

Example

## test passed - test_multiSeqAsOne
Replidec -p test_multiSeqAsOne

## test passsed - test_multiSeqEachAsOne
Replidec -p test_multiSeqEachAsOne

## test passsed - test_batch
Replidec -p test_batch

## 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