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
pip install tkp-findertkp-finder is distributed under the terms of the MIT license.
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.