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https://github.com/edikedik/tkp-finder
A command-line tool to discover and annotate tandem protein kinases.
https://github.com/edikedik/tkp-finder
Last synced: about 2 months ago
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A command-line tool to discover and annotate tandem protein kinases.
- Host: GitHub
- URL: https://github.com/edikedik/tkp-finder
- Owner: edikedik
- License: mit
- Created: 2022-11-16T13:37:24.000Z (about 2 years ago)
- Default Branch: master
- Last Pushed: 2022-12-22T14:28:13.000Z (about 2 years ago)
- Last Synced: 2024-11-08T02:49:25.563Z (about 2 months ago)
- Language: Python
- Size: 3.78 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# tkp-finder
[](https://pypi.org/project/tkp-finder)
[](https://pypi.org/project/tkp-finder)
`tkp-finder` is a CLI tool to discover and annotate tandem protein kinases.
It's based on [lXtractor]() -- a general-purpose library for data mining from sequences and structures.
The latter is under active development, so bugs are possible.
-----
**Table of Contents**
- [Installation](#installation)
- [License](#license)
- [Usage](#usage)
## Installation
```console
pip install tkp-finder
```
## License
`tkp-finder` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.
## Usage
The installation should make the script `tkp-finder` globally available.
The interface has two commands:
The `setup` command will download and prepare HMM models for annotation.
```
→ tkp-finder setup --help
Usage: tkp-finder setup [OPTIONS]
Command to initialize the HMM data needed for TKPs' annotation.
Options:
-H, --hmm_dir DIRECTORY Path to a directory to store hmm-related data.
[required]
-d, --download If True, download the Pfam data from interpro.
-q, --quiet Disable verbose output.
--path_pfam_a FILE A path to downloaded Pfam-A HMM profiles. By
default, if `download` is ``False``,will try to
find it within the `hmm_dir`.
--path_pfam_dat FILE A path to downloaded Pfam-A (meta)data file. By
default, if `download` is ``False``,will try to
find it within the `hmm_dir`.
-h, --help Show this message and exit.
```
For the first-time usage, invoke
```
→ tkp-finder setup -H hmm -d
```
This will download Pfam-A HMMs and accompanying metadata, and split the models into categories.
The resulting directory:
```
→ tree -L 2 hmm
hmm
├── PF00069.hmm
├── Pfam-A.hmm
├── Pfam-A.hmm.dat
├── pfam_entries.tsv
└── profiles
├── Coiled-coil
├── Disordered
├── Domain
├── Family
├── Motif
├── Repeat
└── unknown
```
To dicover and annotate TKPs, refer to `tkp-finder find` command:
```
→ tkp-finder find --help
Usage: tkp-finder find [OPTIONS] [FASTA]...
Options:
-H, --hmm_dir DIRECTORY Directory with HMM profiles. Expected to contain
`profiles` dir and target PK profile
(PF00069.hmm). See `tkp-finder setup` on how to
prepare this dir.
-t, --hmm_type TEXT Which HMM types to use for annotating the
discovered TKPs. The names must correspond to
folders within he `hmm_dir`. [default: Family,
Domain, Motif]
-p, --pk_profile FILE A path to the PK HMM profile. By default, will
try to find it within the `hmm_dir`.
-m, --motif TEXT A motif to discriminate between PKs and pseudo
PKs. This corresponds to the following conserved
elements:: (1) b3-Lys(2) aC-helix Glu(3-4-5) HRD
motif(6-7-8) DFG motif [default: KEXXDDXX]
-o, --output DIRECTORY Output directory to store the results. Be
default, will store within `./tkp-finder`.
-n, --num_proc INTEGER The number of cpus for data parallelism: each
input fasta will be annotated within separate
process. HINT: one may split large fasta files
for faster processing.
-q, --quiet Disable logging and progress bar
--pk_map_name TEXT Use this name for the protein kinase domain.
[default: PK]
--ppk_map_name TEXT Use this name for pseudo protein kinases.
[default: PPK]
--min_domain_size INTEGER The minimum number of amino acid residues within
a PK domain. [default: 150]
--min_domains INTEGER The number of domains to classify a protein as
TKP.
--timeout INTEGER For parallel processing, indicate timeout for
getting results of a single process.
-h, --help Show this message and exit.
```