Ejemplo n.º 1
0
        private void search_additional_lipidmaps_in_lipidmaps()
        {
            List <metabolite> tmpListOfMetab = new List <metabolite>();

            if (metabolites.List_metabolites.Select(x => x.Lipidmaps_id).Intersect(In_add_Lipidmaps_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any())
            {
                Parallel.ForEach(In_add_Lipidmaps_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x)), addLipidmaps =>
                {
                    if (metabolites.List_metabolites.Any(x => x.Lipidmaps_id == addLipidmaps))
                    {
                        tmpListOfMetab.Add(metabolites.List_metabolites.Where(x => x.Lipidmaps_id == addLipidmaps).OrderByDescending(x => x.List_of_pathways.Count).First());
                    }
                });
            }

            if (tmpListOfMetab.Count > 1)
            {
                outputToLog.WriteLine("more than one compounds in DB file for additional LipidMaps_ID=" + string.Join("|", In_add_Lipidmaps_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))));
            }
            ToHMDB_metabolite(tmpListOfMetab.OrderByDescending(x => x.List_of_pathways.Count).First());
        }
Ejemplo n.º 2
0
        public void getFromMetaboliteDB()
        {
            //here the idea is as follows
            //first search with primary hmdb, cas, kegg, chebi, pubchem, chemspider, lipidmaps and metlin in the all metabolites list on primary hmdb, cas, kegg, chebi, pubchem, chemspider, lipidmaps and metlin ids respectively
            //if nothing found search with primary hmdb, cas, kegg and chebi in the all metabolites list on additional (secodnary) hmdb, cas, kegg and chebi ids respectively
            //if nothing found search with additional (secondary) hmdb, cas, kegg, chebi, pubchem, chemspider, lipidmaps and metlin in the all metabolites list on primary and additional (secodnary) hmdb, cas, kegg, chebi, pubchem, chemspider, lipidmaps and metlin ids respectively

            if (!string.IsNullOrEmpty(In_Hmdb_id) && !string.IsNullOrWhiteSpace(In_Hmdb_id) && metabolites.List_metabolites.Any(x => x.Hmdb_accession == In_Hmdb_id))
            {
                search_hmdb_in_hmdb_id();
            }
            else if (!string.IsNullOrEmpty(In_Cas_id) && !string.IsNullOrWhiteSpace(In_Cas_id) && metabolites.List_metabolites.Any(x => x.Cas_registry_number == In_Cas_id))
            {
                search_cas_in_cas_id();
            }
            else if (!string.IsNullOrEmpty(In_Kegg_id) && !string.IsNullOrWhiteSpace(In_Kegg_id) && metabolites.List_metabolites.Any(x => x.Kegg_id == In_Kegg_id))
            {
                search_kegg_in_kegg_id();
            }
            else if (!string.IsNullOrEmpty(In_Chebi_id) && !string.IsNullOrWhiteSpace(In_Chebi_id) && metabolites.List_metabolites.Any(x => x.Chebi_id == In_Chebi_id))
            {
                search_chebi_in_chebi_id();
            }
            else if (!string.IsNullOrEmpty(In_Pubchem_id) && !string.IsNullOrWhiteSpace(In_Pubchem_id) && metabolites.List_metabolites.Any(x => x.Pubchem_compound_id == In_Pubchem_id))
            {
                search_pubchem_in_pubchem_id();
            }
            else if (!string.IsNullOrEmpty(In_Chemspider_id) && !string.IsNullOrWhiteSpace(In_Chemspider_id) && metabolites.List_metabolites.Any(x => x.Chemspider_id == In_Chemspider_id))
            {
                search_chemspider_in_chemspider_id();
            }
            else if (!string.IsNullOrEmpty(In_Lipidmaps_id) && !string.IsNullOrWhiteSpace(In_Lipidmaps_id) && metabolites.List_metabolites.Any(x => x.Lipidmaps_id == In_Lipidmaps_id))
            {
                search_lipidmaps_in_lipidmaps_id();
            }
            else if (!string.IsNullOrEmpty(In_Metlin_id) && !string.IsNullOrWhiteSpace(In_Metlin_id) && metabolites.List_metabolites.Any(x => x.Metlin_id == In_Metlin_id))
            {
                search_metlin_in_metlin_id();
            }
            else if (!string.IsNullOrEmpty(In_Hmdb_id) && !string.IsNullOrWhiteSpace(In_Hmdb_id) && metabolites.List_metabolites.SelectMany(x => x.Hmdb_secondary_accessions).Any(x => x == In_Hmdb_id))
            {
                search_hmdb_in_additional_hmdb_id();
            }
            else if (!string.IsNullOrEmpty(In_Cas_id) && !string.IsNullOrWhiteSpace(In_Cas_id) && metabolites.List_metabolites.SelectMany(x => x.Cts_cas).Any(x => x == In_Cas_id))
            {
                search_cas_in_additional_cas_id();
            }
            else if (!string.IsNullOrEmpty(In_Kegg_id) && !string.IsNullOrWhiteSpace(In_Kegg_id) && metabolites.List_metabolites.SelectMany(x => x.Cts_kegg).Any(x => x == In_Kegg_id))
            {
                search_kegg_in_additional_kegg_id();
            }
            else if (!string.IsNullOrEmpty(In_Chebi_id) && !string.IsNullOrWhiteSpace(In_Chebi_id) && metabolites.List_metabolites.SelectMany(x => x.Cts_chebi).Any(x => x == In_Chebi_id))
            {
                search_chebi_in_additional_chebi_id();
            }
            else if (In_add_Hmdb_id.Count > 0 &&
                     (metabolites.List_metabolites.Select(x => x.Hmdb_accession).Intersect(In_add_Hmdb_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any() ||
                      metabolites.List_metabolites.SelectMany(x => x.Hmdb_secondary_accessions).Intersect(In_add_Hmdb_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any()))
            {
                search_additional_hmdb_in_hmdb_and_additional_hmdb_id();
            }
            else if (In_add_Cas_id.Count > 0 &&
                     (metabolites.List_metabolites.Select(x => x.Cas_registry_number).Intersect(In_add_Cas_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any() ||
                      metabolites.List_metabolites.SelectMany(x => x.Cts_cas).Intersect(In_add_Cas_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any()))
            {
                search_additional_cas_in_cas_and_additional_cas_id();
            }
            else if (In_add_Kegg_id.Count > 0 &&
                     (metabolites.List_metabolites.Select(x => x.Kegg_id).Intersect(In_add_Kegg_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any() ||
                      metabolites.List_metabolites.SelectMany(x => x.Cts_kegg).Intersect(In_add_Kegg_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any()))
            {
                search_additional_kegg_in_kegg_and_additional_kegg_id();
            }
            else if (In_add_Chebi_id.Count > 0 &&
                     (metabolites.List_metabolites.Select(x => x.Chebi_id).Intersect(In_add_Chebi_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any() ||
                      metabolites.List_metabolites.SelectMany(x => x.Cts_chebi).Intersect(In_add_Chebi_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any()))
            {
                search_additional_chebi_in_chebi_and_additional_chebi_id();
            }
            else if (In_add_Pubchem_id.Count > 0 &&
                     metabolites.List_metabolites.Select(x => x.Pubchem_compound_id).Intersect(In_add_Pubchem_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any())
            {
                search_additional_pubchem_in_pubchem();
            }
            else if (In_add_Chemspider_id.Count > 0 &&
                     metabolites.List_metabolites.Select(x => x.Chemspider_id).Intersect(In_add_Chemspider_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any())
            {
                search_additional_chemspider_in_chemspider();
            }
            else if (In_add_Lipidmaps_id.Count > 0 &&
                     metabolites.List_metabolites.Select(x => x.Lipidmaps_id).Intersect(In_add_Lipidmaps_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any())
            {
                search_additional_lipidmaps_in_lipidmaps();
            }
            else if (In_add_Metlin_id.Count > 0 &&
                     metabolites.List_metabolites.Select(x => x.Metlin_id).Intersect(In_add_Metlin_id.Where(x => !string.IsNullOrEmpty(x) && !string.IsNullOrWhiteSpace(x))).Any())
            {
                search_additional_metlin_in_metlin();
            }
            else
            {
                add_not_found_metabolite();
                return;
            }
        }