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.

Metadata

Release files for findltr 0.0.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for findltr 0.0.2
File	Size	Uploaded	Provenance	Actions
findltr-0.0.2.tar.gz	7.2 kB	Oct 26, 2015	Without provenance	Details for findltr-0.0.2.tar.gz

Release files / findltr-0.0.2.tar.gz

Download URL	findltr-0.0.2.tar.gz
Size	7.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`a6f84d2fe35f9de0afcbf421044c1630cfea4fb55d105b2907590f924be6fea7`
BLAKE2b-256 checksum How to use checksums	`5b45b999d59695b46c56d31f858fd1e0c18a88c2f2dbcf783685e6a75ab41605`
Upload date	Oct 26, 2015
Uploaded using Trusted Publishing? What is trusted publishing?	No

Security for findltr 0.0.2

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This release

0.0.2 This release

Oct 26, 2015 1 release file No provenance

0.0.1