معرفی شرکت ها
Replidec-0.2.3.1
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مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
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مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Replication Cycle Detector for Phages
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | Replidec-0.2.3.1 |
| نام | Replidec |
| نسخه کتابخانه | 0.2.3.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Xue Peng |
| ایمیل نویسنده | xue.peng@helmholtz-muenchen.de |
| آدرس صفحه اصلی | https://github.com/deng-lab/Replidec |
| آدرس اینترنتی | https://pypi.org/project/Replidec/ |
| مجوز | MIT license |
# Replidec: Replication Cycle Detector for Phages
[](https://pypi.python.org/pypi/Replidec)
[](https://anaconda.org/denglab/replidec)
[](https://anaconda.org/denglab/replidec)
[](https://anaconda.org/denglab/replidec)
## Aim
Use bayes classifier combine with homology search to predict virus replication cycle
## Install
Download database from https://zenodo.org/record/6857082/files/db.tar.gz
### Method 1: using Docker (recommended)
```bash
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,
```bash
singularity pull replidec.sif docker://denglab/replidec
```
### Method 2: using Conda
```bash
conda create -n replidec
conda activate replidec
conda install -c denglab -c conda-forge 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+
```bash
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]
```
## Usage: database
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. '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
```
نیازمندی
| مقدار | نام |
|---|---|
| >=1.77 | biopython |
| >=0.18.2 | future |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl Replidec-0.2.3.1:
pip install Replidec-0.2.3.1.whl
نصب پکیج tar.gz Replidec-0.2.3.1:
pip install Replidec-0.2.3.1.tar.gz