findltr 0.0.1

Search for LTR retrotransposons.

findltr

Command-line tool for de novo identification of LTR retrotransposons.

Requirements

• Basic Local Alignment Search Tool (BLAST):

  $ sudo apt-get install ncbi-blast+

Installations

Example install, using VirtualEnv:

# install/use python virtual environment
virtualenv ~/virtenv_scratch --no-site-packages

# activate the virtual environment
source ~/virtenv_scratch/bin/activate

# upgrade pip in the new virtenv
pip install -U pip setuptools

# install this package in DEVELOPMENT mode
python setup.py develop

# or simply install
# python setup.py install

Options

The list of available options:

General

--input

Input *.fasta or *.fa file

--output

Output *.gff file

Search parameters

Option	Description	Default
–algorithm	Algorithm, [kmp|salcp|original]	original
–pattern_len	Length of pattern	20
–min_distance	Minimal distance between LTRs	1000
–max_distance	Maximal distance between LTRs	20000
–min_ltr_len	Minimal length of LTRs	100
–max_ltr_len	Maximal length of LTRs	1000

Other

--verbose

Include more details

--debug

Turn on debugging output, do not catch exceptions

See findltr --help for complete list of available options.