https://github.com/gamcil/frippa
Fungal Ribosimally synthesized and Post-translationally modified Peptide (RiPP) assayer
https://github.com/gamcil/frippa
Last synced: about 1 year ago
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Fungal Ribosimally synthesized and Post-translationally modified Peptide (RiPP) assayer
- Host: GitHub
- URL: https://github.com/gamcil/frippa
- Owner: gamcil
- License: mit
- Created: 2019-09-25T06:33:51.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2021-12-14T04:31:16.000Z (over 4 years ago)
- Last Synced: 2025-06-12T18:05:52.837Z (about 1 year ago)
- Language: Python
- Size: 156 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# frippa
Fungal Ribosimally synthesized and Post-translationally modified Peptide (RiPP) assayer
## Installation
The quickest way to start using fRiPPa is by using Docker. Note that due to licensing,
you have to grab your own copy of SignalP 5.0b first ([here](https://services.healthtech.dtu.dk/software.php)).
First, download the [fRiPPa Dockerfile](https://raw.githubusercontent.com/gamcil/frippa/master/Dockerfile)
and place it in the same directory as your downloaded copy of SignalP. You should have
the following files:
```
Dockerfile
signalp-5.0b.Linux.tar.gz
```
Then, you can build a Docker image by:
```
docker build -t frippa -f Dockerfile .
```
Once you have built the image, the easiest way to use it is by using the [wrapper BASH
script](https://raw.githubusercontent.com/gamcil/frippa/master/frippa-docker). For
example:
```sh
wget https://raw.githubusercontent.com/gamcil/frippa/master/frippa-docker
chmod +x frippa-docker
frippa-docker genome.gbk
```
This will download the wrapper script, ``frippa-docker``, make it executable, and run
it on ``genome.gbk``. You can put this script somewhere on your system ``$PATH`` to
access it from anywhere.
The wrapper script will mount the present working directory (``$PWD``; the directory
you're in when you launched ``frippa-docker``) as the working directory, allowing you to
pass files between the host system and the docker container. Note: files must be
somewhere **inside** the ``$PWD``; using e.g. ``../path/outside/pwd`` will not work.
Under the hood, this is the equivalent of:
```sh
WORKDIR="${PWD}"
MOUNT="type=bind,source=${WORKDIR},target=${WORKDIR}"
docker run --rm "${IT[@]}" \
--workdir "${WORKDIR}" \
--mount "${MOUNT}" \
frippa \
frippa genome.gbk
```
## Usage
```
usage: frippa [-h] [-o OUTPUT] [-t THREADS] [-e EVALUE] [-n NEIGHBOURS]
[-v OVERLAP] [-ra] [-cp CUTSITE_PCT] [-mr MIN_REPEATS]
[-min_rl MIN_REPEAT_LENGTH] [-max_rl MAX_REPEAT_LENGTH]
[-rs REPEAT_SIMILARITY] [-zc Z_SCORE_CUTOFF]
genbank
positional arguments:
genbank Input GenBank file
optional arguments:
-h, --help show this help message and exit
-o OUTPUT, --output OUTPUT
Path to write results to
-t THREADS, --threads THREADS
How many threads to use when running hmmsearch and
SignalP
-e EVALUE, --evalue EVALUE
E-value cutoff to use when filtering hmmsearch results
Cluster prediction settings:
-n NEIGHBOURS, --neighbours NEIGHBOURS
Number of base pair either side of a DUF3328 hit to
grab proteins
-v OVERLAP, --overlap OVERLAP
Maximum percentage of overlapping proteins before
clusters are merged
-ra, --report_all Report all clusters with DUF3328 hits, even if no
repeat predictions
Repeat filtering:
-cp CUTSITE_PCT, --cutsite_pct CUTSITE_PCT
Threshold for total cut sites in individual repeats
-mr MIN_REPEATS, --min_repeats MIN_REPEATS
Minimum number of detected repeats
-min_rl MIN_REPEAT_LENGTH, --min_repeat_length MIN_REPEAT_LENGTH
Minimum length of a repeat sequence.
-max_rl MAX_REPEAT_LENGTH, --max_repeat_length MAX_REPEAT_LENGTH
Maximum length of a repeat sequence. Long sequences
tend to be red herrings
-rs REPEAT_SIMILARITY, --repeat_similarity REPEAT_SIMILARITY
Average (hamming) similarity threshold for repeat
sequences
-zc Z_SCORE_CUTOFF, --z_score_cutoff Z_SCORE_CUTOFF
Minimum z-score for a repeat sequence
```
Note that you will have to provid
## Dependencies
fRiPPa requires all following tools to be available on the system $PATH:
### lfasta from the FASTA2 package
```
mkdir fasta2
cd fasta2
wget http://faculty.virginia.edu/wrpearson/fasta/fasta2/fasta2.shar.Z
gunzip fasta2.shar.Z
sh fasta2.shar
make lfasta
```
### RADAR
Download latest release from GitHub (https://github.com/AndreasHeger/radar/releases)
```
tar -xvzf radar-x.x.x.tgz
cd radar-x.x.x.tgz
./configure
make; make install
```
### SignalP 5.0
Obtain executable from: https://services.healthtech.dtu.dk/software.php
### hmmsearch from HMMER
Obtain from: http://hmmer.org/