cmkobel / kofam_scan

CLI tool to annotate genes with KOfam

KofamScan

KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. Online version is available on https://www.genome.jp/tools/kofamkoala/ .

Requirements

• Linux
• Ruby >= 2.4
• HMMER >= 3.1
• GNU Parallel

If you wish to use Conda for managing dependencies, you can use the bundled environment.yml file to install these dependencies with conda env create -n kofam_scan -f environment.yml.

Usage

1. Download KOfam database from ftp://ftp.genome.jp/pub/db/kofam/ and decompress it. You will get profile HMMs in profiles/ directory and ko_list.
2. Create config.yml in the same directory as exec_annotation script. See below for details.
3. Execute exec_annotation.

$ ./exec_annotation -o result.txt query.fasta

Query file

A query file is a FASTA file with one or more amino acid sequences. You cannot use nucleotide sequences. Each sequence must have a unique name. A name of a sequence is a string between the header symbol (">") and the first blank character (whitespace, tab, line break, etc.). Do not put a whitespace right after ">".

Profiles

Specify the path of the profile database you downloaded by giving --profile option to the command or writing it to config.yml. The path can be a directory, .hmm file, or .hal file. If it is a directory, .hmm files in the directory will be used. If a .hmm file, only the file will be used. If a .hal file, files listed in the .hal file will be used. File paths in a .hal file are either absolute or relative to the directory of the file. Lines start with # are ignored.

KOfam has prokaryote.hal and eukaryote.hal in profiles directory. They are lists of profiles excluding eukaryote- and prokaryote-specific KOs respectively. If you are interested in only several KOs, you can make your original .hal file and use it as a database. It will reduce computation time.

Options

• -o FILE
  • The result are output to FILE. It defaults to stdout.
• -p, --profile=PROFILE
  • Use PROFILE as a profile database. See Profiles
• -k, --ko-list=FILE
  • Use FILE as a KO list.
• --cpu=N
  • Set the number of hmmsearch processes started simultaneously to N. It defaults to 1 unless it is set in config.yml.
• -c FILE
  • Use FILE as a config file instead of config.yml in the same directory as exec_annotation.
• --tmp-dir=DIR
  • Use DIR as a temporary directory where hmmsearch results are. It will be created if not exist. It defaults to ./tmp.
• -E, --e-value=VALUE
  • Require E-value to be smaller than or equal to VALUE. If not, an asterisk will not be added in detail format or the hit will not be reported in other formats.
• -T, --threshold-scale=VALUE
  • The score thresholds are multiplied by VALUE. For example, with -T2 option, the thresholds become twice as strict.
• -f, --format=FORMAT
  • Set the format of the output to FORMAT. Three formats below are available.
  • detail
    • Default format. Gene name, assigned K number, threshold of the KO, hmmsearch score and E-value, and the definition of KO are shown. In addition, an asterisk '*' is added to the head of the line if the score is higher than the threshold.
  • detail-tsv
    • Tab separated values for detail format.
  • mapper
    • Format which can be used for KEGG Mapper input. It includes a gene name and an assigned K number separated by a tab. Here, an assigned K number represents a hit with score above the predefined threshold. Note that for some KOs, predefined score thresholds are not available when they are represented by a very few number of sequences in KEGG GENES.
  • mapper-oneline
    • Similar to mapper, but when more than one KO are assigned to a gene, all assigned KO are shown in one line separated by tabs.
• --[no-]report-unannotated
  • With --report-unannotated option, gene names are shown even when no KO is assigned (default when --format=mapper(-oneline)). With --no-report-unannotated such genes are not shown at all (default when --format=detail).
• --create-alignment
  • hmmsearch's normal outputs per profile are stored in the temporary directory. In addition, domain information and alignments in the outputs will be rearranged per query.
  • Not compatible with --reannotation
• -r, --reannotation
  • Skip hmmsearch and assume that hmmsearch outputs are already in the temporary directory. This will help you to make an output in a different format or redo annotation changing thresholds.
  • Not compatible with --create-alignment
• -h, --help
  • Show brief help message.

config.yml

The following variables can be set by config.yml.

• profile
  • Path to KOfam profiles.
  • --profile option takes precedence.
• ko_list
  • Path to the KO list of KOfam.
  • --ko-list option takes precedence.
• cpu
  • Number of hmmsearch processes started simultaneously.
  • --cpu option takes precedence.
• hmmsearch
  • Path to hmmsearch executable. If not given, it will be searched for PATH.
• parallel
  • Path to parallel executable. If not given, it will be searched for PATH.

License

This software is released under the MIT License.