Fast implementation of KofamScan optimized for high-memory systems using PyHmmer. PyKofamSearch can handle fasta in uncompressed or gzip format and databases in either HMM or Python pickle serialized format. No intermediate files are created.
pip install pykofamsearch
- pyhmmer >=0.10.12
- pandas
- tqdm
| Database | Tool | Single Threaded | 12 Threads |
|---|---|---|---|
| Full Database | PyKofamSearch | 21:34 | 2:45 |
| KofamScan | 21:53 | 3:40 | |
| Enzymes | PyKofamSearch | 7:39 | 0:56 |
* Time in minutes for 4977 proteins in test/test.faa.gz.
Official benchmarking for hmmsearch algorithm implemented in PyHMMER against HMMER from Larralde et al. 2023:
Recommended usage for PyKOfamSearch is on systems with 1) high RAM; 2) large numbers of threads; and/or 3) reading/writing to disk is charged (e.g., AWS EFS). Also useful when querying a large number of proteins.
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# Download and serialize database serialize_kofam_models -o path/to/database_directory/# Download database DATABASE_DIRECTORY=/path/to/database_directory/ mkdir -p ${DATABASE_DIRECTORY}/Annotate/KOfam/ wget -v -O - ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz | gzip -d > ${DATABASE_DIRECTORY}/Annotate/KOfam/ko_list wget -v -c ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz -O - | tar -xz mv profiles ${DATABASE_DIRECTORY}/Annotate/KOfam/ # Serialize database serialize_kofam_models -d path/to/profiles/ -k path/to/ko_list -b path/to/database.pkl.gz
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# Run PyKofamSearch pykofamsearch -i test/test.faa.gz -o output.tsv -d ${DATABASE_DIRECTORY}/Annotate/KOfam -p=-1
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Database can be uncompressed pickle or gzipped pickle.
# Full database pykofamsearch -i test/test.faa.gz -o output.tsv -b ~/Databases/KOfam/database.pkl.gz -p=-1 # Enzymes only pykofamsearch -i test/test.faa.gz -o output.enzymes.tsv -b ~/Databases/KOfam/database.enzymes.pkl.gz -p=-1
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reformat_pykofamsearch -i pykofamsearch_output.tsv -o pykofamsearch_output.reformatted.tsv
$ pykofamsearch -h
usage: pykofamsearch -i <proteins.fasta> -o <output.tsv> -d
Running: pykofamsearch v2024.4.18 via Python v3.10.14 | /Users/jolespin/miniconda3/envs/kofamscan_env/bin/python3.10
options:
-h, --help show this help message and exit
I/O arguments:
-i PROTEINS, --proteins PROTEINS
path/to/proteins.fasta. stdin does not stream and loads everything into memory. [Default: stdin]
-o OUTPUT, --output OUTPUT
path/to/output.tsv [Default: stdout]
--no_header No header
Utility arguments:
-p N_JOBS, --n_jobs N_JOBS
Number of threads to use [Default: 1]
HMMSearch arguments:
-e EVALUE, --evalue EVALUE
E-value threshold [Default: 0.1]
-a, --all_hits Return all hits and do not use curated threshold. Not recommended for large queries.
Database arguments:
-d DATABASE_DIRECTORY, --database_directory DATABASE_DIRECTORY
path/to/kofam_database_directory/ cannot be used with -b/-serialized_database
-b SERIALIZED_DATABASE, --serialized_database SERIALIZED_DATABASE
path/to/database.pkl cannot be used with -d/--database_directory
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From pykofamsearch:
id_protein id_ko threshold score e-value definition SRR13615825__k127_135326_1 K00012 377.73 6.245e+02 7.34282e-188 UDPglucose 6-dehydrogenase [EC:1.1.1.22] SRR13615825__k127_87070_1 K00012 377.73 4.751e+02 1.15847e-142 UDPglucose 6-dehydrogenase [EC:1.1.1.22] SRR13615825__k127_278295_3 K00020 348.7 3.639e+02 5.39377e-109 3-hydroxyisobutyrate dehydrogenase [EC:1.1.1.31] SRR13615825__k127_23043_1 K00033 157.6 3.598e+02 8.14325e-108 6-phosphogluconate dehydrogenase [EC:1.1.1.44 1.1.1.343] SRR13615825__k127_278295_3 K00042 389.27 3.941e+02 2.58098e-118 2-hydroxy-3-oxopropionate reductase [EC:1.1.1.60] -
From reformat_pykofamsearch:
id_protein number_of_hits ids names evalues scores SRR13615825__k127_135326_1 1 ['K00012'] ['UDPglucose 6-dehydrogenase [EC:1.1.1.22]'] [7.34282e-188] [624.5] SRR13615825__k127_87070_1 1 ['K00012'] ['UDPglucose 6-dehydrogenase [EC:1.1.1.22]'] [1.15847e-142] [475.1] SRR13615825__k127_278295_3 2 ['K00020', 'K00042'] ['3-hydroxyisobutyrate dehydrogenase [EC:1.1.1.31]', '2-hydroxy-3-oxopropionate reductase [EC:1.1.1.60]'] [5.39377e-109, 2.58098e-118] [363.9, 394.1] SRR13615825__k127_23043_1 1 ['K00033'] ['6-phosphogluconate dehydrogenase [EC:1.1.1.44 1.1.1.343]'] [8.14325e-108] [359.8] SRR13615825__k127_72951_1 1 ['K00053'] ['ketol-acid reductoisomerase [EC:1.1.1.86]'] [1.54591e-108] [362.2] -
From reformat_pykofamsearch with -b/--best_hits_only:
id_protein id name evalue score SRR13615825__k127_135326_1 K00012 UDPglucose 6-dehydrogenase [EC:1.1.1.22] 7.34282e-188 624.5 SRR13615825__k127_87070_1 K00012 UDPglucose 6-dehydrogenase [EC:1.1.1.22] 1.15847e-142 475.1 SRR13615825__k127_278295_3 K00042 2-hydroxy-3-oxopropionate reductase [EC:1.1.1.60] 2.58098e-118 394.1 SRR13615825__k127_23043_1 K00033 6-phosphogluconate dehydrogenase [EC:1.1.1.44 1.1.1.343] 8.14325e-108 359.8 SRR13615825__k127_72951_1 K00053 ketol-acid reductoisomerase [EC:1.1.1.86] 1.54591e-108 362.2
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Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, Ogata H. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020 Apr 1;36(7):2251-2252. doi: 10.1093/bioinformatics/btz859. PMID: 31742321; PMCID: PMC7141845.
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Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011 Oct;7(10):e1002195. doi: 10.1371/journal.pcbi.1002195. Epub 2011 Oct 20. PMID: 22039361; PMCID: PMC3197634.
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Larralde M, Zeller G. PyHMMER: a Python library binding to HMMER for efficient sequence analysis. Bioinformatics. 2023 May 4;39(5):btad214. doi: 10.1093/bioinformatics/btad214. PMID: 37074928; PMCID: PMC10159651.
PyKOfamSearch output is slightly different than KofamScan. For example, in the test case the number of significant hits from KofamScan is 1188 while PyKofamSearch is 1190. All hits in from KofamScan are in PyKOfamSearch output.
The code for PyKOfamSearch is licensed under an MIT License
Please contact jolespin@newatlantis.io regarding any licensing concerns.