File formats

deepnog uses standard file formats, as detailed below for eggNOG 5 (1239, Firmicutes) data.

Protein sequences

Protein sequences are expected in FASTA format. Each entry must contain a unique record ID. That is, a user_data.faa should look like this:

>1000569.HMPREF1040_0002
MMKHDDHVHQIRTEPIYAILGETFSRGRTNRQVAKALLGAGVRIIQYREKEKSWQEKYEE
ARDICQWCNEYGATFIMNDSIDLAIACEAPAIHVGQDDAPVAWVRRLAQRDIVVGVSTHT
IAEMKKAVRDGADYVGLGPMYQTTSKMDVHDIVADVDKAYALTLPIPVVTIGGIDLIHIR
QLYTEGFRSFAMISALVGATDIVEQIGAFRQVLQEKIDEC
>1000569.HMPREF1040_0003
MATTVGDIVTYLQGIAPLYLKEEWDNPGLLLGNQGDPVSSVLVTLDVMEGTVDYAIAEGI
SFIFSHHPLIMKGIKAIRTDSYDGRMYQKLLSHHIAVYAAHTNLDSATGGVNDVLAEHLQ
LQHVRPFIPGVSESLYKIAIYVPKGYGDAIREVLGKHDAGHLGAYSYCSFSVAGQGRFKP
LAGTHPFIGKRDVLETVEEERIETIVEGSRLGEVITAMLAVHPYEEPAYDIYPLYQQRTA
LGLGRLGELATPLSSMAAVQWVKEALHLTHVSYAGPMDRQIQTIAVLGGSGAEFIATAKA
AGATLYVTGDMKYHAAQEAIKQGILVVDAGHFGTEFPVIDRMKQNIEAENEKQGWHIQCV
VDPTAMDMIQRL

Compression is allowed (user_data.faa.gz, or user_data.faa.xz). For typical usage of deepnog infer for protein orthologous group assignments this is already sufficient.

Protein orthologous group labels

Training new models with deepnog train, or assessing model quality with deepnog infer --test_labels require providing the orthologous group labels.

File format is CSV (comma-separated values) with a preceding header line, and three columns (index, sequence record ID, orthologous group ID).

,string_id,eggnog_id
1543720,1121929.KB898683_gene1916,1V3NB
351865,536232.CLM_3459,1TPCN
[...]
1570381,1000569.HMPREF1040_0002,1V3ZR
744166,1000569.HMPREF1040_0003,1TQ27
[...]
426023,1423743.JCM14108_56,1TPGE

To construct some user_data.csv:

  • Copy (do not modify) the header line.

  • Provide an index in the first column (e.g. 1..N; currently unused, but required).

  • Provide the sequence ID (e.g. eggNOG/STRING ID) in column 2.

  • Provide its corresponding group label in column 3.

  • Sequence IDs in column 2 must match the IDs used in the user_data.faa.

Assignment output

Orthologous group assignments are output in tabular format (comma-separated).

  • Column 1: Sequence ID

  • Column 2: Assignment/Orthologous group

  • Column 3: Assignment confidence in 0..1 (higher=better).

Example:

sequence_id,prediction,confidence
1000565.METUNv1_00038,COG0466,1.0
1000565.METUNv1_00060,COG0500,0.20852506
1000565.METUNv1_00091,COG0810,0.9999591
1000565.METUNv1_00093,COG0659,1.0
1000565.METUNv1_00103,COG5000,0.70716757
1000565.METUNv1_00105,COG0346,0.9999982
1000565.METUNv1_00106,COG3791,1.0
1000565.METUNv1_00114,COG0239,1.0
1000565.METUNv1_00115,COG1643,1.0