diff --git a/lib/commands/unipept.ts b/lib/commands/unipept.ts index b70718f6..3c299050 100644 --- a/lib/commands/unipept.ts +++ b/lib/commands/unipept.ts @@ -2,6 +2,7 @@ import { BaseCommand } from './base_command.js'; import { Pept2ec } from './unipept/pept2ec.js'; import { Pept2funct } from './unipept/pept2funct.js'; import { Pept2go } from './unipept/pept2go.js'; +import { Pept2interpro } from './unipept/pept2interpro.js'; import { Pept2lca } from './unipept/pept2lca.js'; export class Unipept extends BaseCommand { @@ -25,6 +26,7 @@ The command will give priority to the first way the input is passed, in the orde .addCommand(new Pept2ec().command) .addCommand(new Pept2funct().command) .addCommand(new Pept2go().command) + .addCommand(new Pept2interpro().command) .addCommand(new Pept2lca().command); } diff --git a/lib/commands/unipept/pept2go.ts b/lib/commands/unipept/pept2go.ts index 8f91128d..c14fcf15 100644 --- a/lib/commands/unipept/pept2go.ts +++ b/lib/commands/unipept/pept2go.ts @@ -3,7 +3,7 @@ import { UnipeptSubcommand } from "./unipept_subcommand.js"; export class Pept2go extends UnipeptSubcommand { - readonly description = `For each tryptic peptide the unipept pept2ec command retrieves from Unipept the set of GO terms from all UniProt entries whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed + readonly description = `For each tryptic peptide the unipept pept2go command retrieves from Unipept the set of GO terms from all UniProt entries whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed - as separate command line arguments - in a text file that is passed as an argument to the -i option diff --git a/lib/commands/unipept/pept2interpro.ts b/lib/commands/unipept/pept2interpro.ts new file mode 100644 index 00000000..f13a03d0 --- /dev/null +++ b/lib/commands/unipept/pept2interpro.ts @@ -0,0 +1,38 @@ +import { Option } from "commander"; +import { UnipeptSubcommand } from "./unipept_subcommand.js"; + +export class Pept2interpro extends UnipeptSubcommand { + + readonly description = `For each tryptic peptide the unipept pept2interpro command retrieves from Unipept the set of InterPro entries from all UniProt entries whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed + +- as separate command line arguments +- in a text file that is passed as an argument to the -i option +- to standard input + +The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.`; + + constructor() { + super("pept2interpro"); + + this.command + .summary("Fetch GO terms of UniProt entries that match tryptic peptides.") + .description(this.description) + .option("-e, --equate", "equate isoleucine (I) and leucine (L) when matching peptides") + .option("-a, --all", "Also return the names of the InterPro entries. Note that this may have a performance penalty.") + .addOption(new Option("-s --select ", "select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.")) + .argument("[peptides...]", "optionally, 1 or more peptides") + .action((args, options) => this.run(args, options)); + } + + requiredFields(): string[] { + return ["peptide"]; + } + + defaultBatchSize(): number { + if (this.options.all) { + return 100; + } else { + return 1000; + } + } +} diff --git a/tests/commands/unipept/pept2interpro.test.ts b/tests/commands/unipept/pept2interpro.test.ts new file mode 100644 index 00000000..5523e7fb --- /dev/null +++ b/tests/commands/unipept/pept2interpro.test.ts @@ -0,0 +1,27 @@ +import { jest } from '@jest/globals'; +import { Pept2interpro } from "../../../lib/commands/unipept/pept2interpro"; + +let output: string[]; +jest + .spyOn(process.stdout, "write") + .mockImplementation((data: unknown) => { output.push(data as string); return true; }); + +beforeEach(() => { + output = []; +}); + +test('test with default args', async () => { + const command = new Pept2interpro(); + await command.run(["AALTER"], { header: true, format: "csv" }); + expect(output[0].startsWith("peptide,total_protein_count,ipr_code,ipr_protein_count")).toBeTruthy(); + expect(output[1].startsWith("AALTER,3310,IPR003613")).toBeTruthy(); + expect(output.length).toBe(2); +}); + +test('test with fasta', async () => { + const command = new Pept2interpro(); + await command.run([">test", "AALTER"], { header: true, format: "csv" }); + expect(output[0].startsWith("fasta_header,peptide,total_protein_count,ipr_code,ipr_protein_count")).toBeTruthy(); + expect(output[1].startsWith(">test,AALTER,3310,IPR003613")).toBeTruthy(); + expect(output.length).toBe(2); +});