#!/usr/bin/env Rscript

# Denes Turei (turei.denes@gmail.com) 2022

library(OmnipathR)
library(dplyr)
library(rlang)

killi <- 105023L

human_killi <-
    ensembl_orthology(
        organism_b = killi,
        attrs_a = 'external_gene_name',
        attrs_b = 'associated_gene_name'
    ) %>%
    select(
        human_ensg = ensembl_gene_id,
        human_genesymbol = external_gene_name,
        killi_ensg = b_ensembl_gene,
        confidence = b_orthology_confidence,
        type = b_orthology_type,
        killi_genesymbol = b_associated_gene_name
    ) %>%
    distinct %>%
    mutate(record_id = 1L:n()) %>%
    translate_ids(
        human_genesymbol = genesymbol,
        human_uniprot = uniprot
    ) %>%
    translate_ids(
        killi_ensg = ensg,
        killi_uniprot = trembl,
        organism = !!killi,
        ensembl = TRUE
    ) %>%
    translate_ids(
        killi_ensg = ensg,
        killi_genesymbol_2 = genesymbol,
        organism = !!killi,
        ensembl = TRUE
    )

human_killi_gs <-
    human_killi %>%
    select(
        human_genesymbol,
        killi_genesymbol
    ) %>%
    filter(
        !is.na(human_genesymbol) &
        !is.na(killi_genesymbol)
    ) %>%
    distinct

killi_uniprot <-
     human_killi %>%
     select(killi_genesymbol, killi_uniprot) %>%
     filter(!is.na(killi_uniprot)) %>%
     distinct

killi_omnipath <-
    import_omnipath_interactions() %>%
    mutate(interaction_record = 1L:n()) %>%
    inner_join(
        human_killi_gs,
        by = c('source_genesymbol' = 'human_genesymbol')
    ) %>%
    select(-source_genesymbol, -source) %>%
    left_join(killi_uniprot, by = 'killi_genesymbol') %>%
    rename(
        source = killi_uniprot,
        source_genesymbol = killi_genesymbol
    ) %>%
    inner_join(
        human_killi_gs,
        by = c('target_genesymbol' = 'human_genesymbol')
    ) %>%
    select(-target_genesymbol, -target) %>%
    left_join(killi_uniprot, by = 'killi_genesymbol') %>%
    rename(
        target = killi_uniprot,
        target_genesymbol = killi_genesymbol
    ) %>%
    relocate(
        source,
        target,
        source_genesymbol,
        target_genesymbol
    )