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======================
findltr

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

Requirements

• Basic Local Alignment Search Tool (BLAST_)::

  $ sudo apt-get install ncbi-blast+

• Genome Tools(GT_) with enabled HMMER option(with-hmmer=yes) via compilation.

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.

.. _BLAST: http://www.ncbi.nlm.nih.gov/books/NBK279690/
.. _GT: https://github.com/genometools/genometools