Merge branch 'master' of https://gitlab.fi.muni.cz/lexa/nested

# nested

#### External tools

## Introduction

*nested* (now also called *TE-greedy*) is software to analyze nested LTR transposable elements 

in DNA sequences, such as reference genomes. It is made of two components: *nested-generator* 

for generating simulated sequences of nested retrotransposons, and *nested-nester* (now called 

*TE-greedy-nester*) that looks for nested, as well as non-nested and solo-LTR repeat sequences 

in the input. Unlike other similar software, *TE-greedy-nester* is structure-based by using 

de-novo retrotransposon identification software *LTR Finder*, relying on sequence information 

only secondarily.

A virtual machine with TE-greedy-nester installed is available at http://hedron.fi.muni.cz/TE-nester_Mint.zip

## External tools

Program is using other external tools. Before usage make sure you have the following tools installed:

- LTR finder (v 1.05+) -

- genometools (v 1.5.8) with gt sketch -

https://github.com/genometools/genometools

#### Install

## Installation - a step-by-step guide

The following is an installation procedure that works on our recent Linux Ubuntu based machines.

### Prerequisites

#### ncbi blast+

```

sudo apt install blast2

```

For user-space installation from source, please, follow https://www.ncbi.nlm.nih.gov/books/NBK279671/ with version 2.2.31+

#### LTR_finder

```

git clone https://github.com/xzhub/LTR_Finder.git

cd LTR_Finder/source

make

```

#### genome tools

```

sudo apt-get install genometools

sudo apt-get install libgenometools0 libgenometools0-dev

```

For user-space installation use:

```

git clone https://github.com/genometools/genometools.git

cd genometools

make -j4

make -j4 install prefix=~/gt

```

See GenomeTools repository for modifications and trouble-shooting of the installation procedure

#### python requirements using pip3

```

sudo pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2

PyYAML==3.12 six==1.11. --no-cache-dir

```

For user-space installation use:

```

pip3 install bcbio-gff==0.6.4 click==6.7 decorator==4.2.1 networkx==2.1 numpy==1.14.2

PyYAML==3.12 six==1.11. --no-cache-dir --user

```

Note1: the version numbers are minimal recommended versions, on many systems you can leave those out.

Note2: With user-space installation of Python software you may need to set PYTONPATH accordingly.

First check its value, not to overwrite something needed by your system:

```

echo $PYTHONPATH

```

Setting can be done with

```

export PYTHONPATH="~/.local/bin"

```

Separate multiple directory entries with a colon.

### TE-greedy-nester

#### clone whole directory from gitlab:

```

git clone https://gitlab.fi.muni.cz/lexa/nested.git

cd nested

```

#### modify respective paths in 'config_template.yml':

```

cp config_template.yml config.yml

vi config.yml

```

Note: we're looking into ways to automate this step

#### after 'config.yml' is created call:

```

chmod +x setup.sh

sudo ./setup.sh

sudo bash ./setup.sh

```

#### Setting up the config

#### For user-space installation of TE-greedy-nester call:

```

bash ./setup.sh --user

```

#### that’s all!

## Setting up the config

Before usage, **config.yml** needs to be set up:

- ltr paths - executable, prosite and tRNAdb

- ltr arguments 

- gt sketch path

- gt sketch arguments

- blastx protein database (our database available at ... )

- ltr finder paths - executable, prosite and tRNAdb

- ltr finder arguments 

- genome tools sketch path

- genome tools sketch arguments

- blastx protein database (installed together with TE-greedy-nester)

- blastx arguments

**Note**: `config.yml` is located by default in directory `/etc/nested/.`

**Note**: `config.yml` is located by default in directory `/etc/nested/.` after 

normal installation or `~/.local/etc/nested/.` after user space installation 

using the --user switch with setup.sh or setup.py 

#### Usage

## Usage

```

Usage: nested-nester [OPTIONS] INPUT_FASTA

__version__ = '1.0.0'

__author__ = 'Radovan Lapár'

__author__ = 'Radovan Lapar, Ivan Vanat, Pavel Jedlicka, Matej Lexa <lexa@fi.muni.cz>'

import yaml

import os.path

from os import path

from os.path import expanduser

with open('/etc/nested/config.yml') as stream:

# depending on whether nester was installed with the --user argument locally or not

home = os.path.expanduser("~")

if path.exists(home + '/.local/etc/nested/config.yml'):

    config_path = home + '/.local/etc/nested/config.yml'

else:

    config_path = '/etc/nested/config.yml'

with open(config_path) as stream:

    config = yaml.load(stream)