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Search for LTR retrotransposons.

Project description

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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+

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.

Project details


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Source Distribution

findltr-0.0.2.tar.gz (7.2 kB view hashes)

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