Installing Databases and Creating Configuration Files

Default Databases

Three databases can be downloaded and formatted automatically when invoking EUKulele. Currently the supported databases are:

To use these databases, all you need to do is specify --database phylodb, --database eukprot, or database mmetsp, respectively, when invoking EUKulele.

Using Other Databases

The basic requirements for using a database with EUKulele are:

  • A singular protein FASTA file containing the sequences

  • A taxonomy table file which contains, for each transcriptome sample in the protein FASTA database:

    • Source_ID: what identifier/organism the transcript came from, which typically should be specified in the header within the FASTA file

    • Supergroup

    • Division

    • Class

    • Order

    • Family

    • Genus

    • Species

  • A JSON file containing a list of dictionary correspondences between each Source ID and transcript ID

    • If you have a separate correspondence between transcript IDs and the organism each transcript ID came from, this prevents you from having to have the Source ID in the transcript header

    • Example: {"CAMPEP_0174983734": "MMETSP0004", "CAMPEP_0174982176": "MMETSP0004", "CAMPEP_0184404416": "MMETSP0007"} for a database of three transcripts coming from two different Source IDs (MMETSP0004 and MMETSP0007)

These files can be generated using the create_protein_file script provided with EUKulele. This script is invoked via:

create-protein-table.py --infile_peptide <peptide fasta file> --infile_taxonomy <taxonomy file> --outfile_json <name of protein map JSON file> --output <name of taxonomy file> [--delim <delimiter> --column <column>]

when EUKulele is installed.

  • --infile_peptide

    • The peptide FASTA file for the database

  • --infile_taxonomy

    • The original taxonomy file

  • --col_source_id

    • Optional; defaults to “Source_ID”; the column in the taxonomy file that corresponds to the Source ID in the database

  • --reformat_tax

    • If this tag is included, the taxonomy will be split according to the contents of the column labeled with the taxonomy_col_id that is specified by the tag below (instead of 7 different columns corresponding to each taxonomic level as in the listing above)

  • --taxonomy_col_id

    • Only relevant if --reformat_tax is specified. The column (e.g. “taxonomy” as in the default) that contains a semicolon-separated list of the taxonomic levels to be separated into columns

  • --outfile_json

    • The name of the output protein map file to be created. To use the output most easily with EUKulele, this file should be called prot-map.json (as is the default) and placed in the same reference directory with the reference protein FASTA file, which ideally would be named reference.pep.fa to facilitate working with the defaults. Then, just specify this output folder as --reference_dir when invoking EUKulele

  • --output

    • The name of the output taxonomy table file to be created. To use the output most easily with EUKulele, this file should be called tax-table.txt (as is the default) and placed in the same reference directory with the reference protein FASTA file, which ideally would be named reference.pep.fa to facilitate working with the defaults. Then, just specify this output folder as --reference_dir when invoking EUKulele

  • --delim

    • What to split the FASTA headers on in the protein database file, typically \t

  • --column

    • The label to be used for the Source_ID parsed from the reference peptide FASTA headers. This is such that the protein map JSON file can be created from the transcript IDs. So if your transcripts include a tab-separated list of entries that includes SOURCE_ID=XXXXX, as in the MMETSP, include a string here for the label before the equals sign. If instead the Source ID occurs at a predictable position in the parsed FASTA headers, a number can be included for this parameter

  • --euk-prot

    • Should only be used if you are specifically creating a table and protein map for the EukProt database, which has a few particular features to take into account

Customizing the Taxonomic Identification Cutoffs

By default, EUKulele uses the following percent identity cutoffs to determine taxonomic matches:

species: 95
genus: 80
family: 65
order: 50
class: 30

To change these cutoffs, simply create a YAML file containing these entries exactly as written above, and provide this cutoff file as input to EUKulele via --cutoff_file <name of YAML file you created>.