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Make "databases" usable in sub-projects
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@martin-steinegger
martin-steinegger committed Oct 1, 2021
1 parent f651879 commit 5afd33c
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153 changes: 153 additions & 0 deletions src/MMseqsBase.cpp
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#include "Command.h"
#include "Parameters.h"
#include "CommandDeclarations.h"
#include "DownloadDatabase.h"

Parameters& par = Parameters::getInstance();
std::vector<Command> baseCommands = {
Expand Down Expand Up @@ -1236,3 +1237,155 @@ std::vector<Command> baseCommands = {
"",
CITATION_MMSEQS2, {{"",DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, NULL}}}
};

#include "databases.sh.h"

std::vector<DatabaseDownload> downloads = {{
"UniRef100",
"The UniProt Reference Clusters provide clustered sets of sequences from the UniProt Knowledgebase.",
"Suzek et al: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23(10), 1282–1288 (2007)",
"https://www.uniprot.org/help/uniref",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"UniRef90",
"The UniProt Reference Clusters provide clustered sets of sequences from the UniProt Knowledgebase.",
"Suzek et al: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23(10), 1282–1288 (2007)",
"https://www.uniprot.org/help/uniref",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"UniRef50",
"The UniProt Reference Clusters provide clustered sets of sequences from the UniProt Knowledgebase.",
"Suzek et al: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23(10), 1282–1288 (2007)",
"https://www.uniprot.org/help/uniref",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"UniProtKB",
"The UniProt Knowledgebase is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.",
"The UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 47(D1), D506-515 (2019)",
"https://www.uniprot.org/help/uniprotkb",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"UniProtKB/TrEMBL",
"UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization.",
"The UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 47(D1), D506-515 (2019)",
"https://www.uniprot.org/help/uniprotkb",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"UniProtKB/Swiss-Prot",
"UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.",
"The UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 47(D1), D506-515 (2019)",
"https://uniprot.org",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"NR",
"Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq.",
"NCBI Resource Coordinators: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46(D1), D8-D13 (2018)",
"https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"NT",
"Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ excluding GSS, STS, PAT, EST, HTG, and WGS.",
"NCBI Resource Coordinators: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46(D1), D8-D13 (2018)",
"https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA",
false, Parameters::DBTYPE_NUCLEOTIDES, databases_sh, databases_sh_len,
{ }
}, {
"GTDB",
"Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus.",
"Parks et al: A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 38(9), 1079–1086 (2020)",
"https://gtdb.ecogenomic.org",
true, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"PDB",
"The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.",
"Berman et al: The Protein Data Bank. Nucleic Acids Res 28(1), 235-242 (2000)",
"https://www.rcsb.org",
false, Parameters::DBTYPE_AMINO_ACIDS, databases_sh, databases_sh_len,
{ }
}, {
"PDB70",
"PDB clustered to 70% sequence identity and enriched using HHblits with Uniclust sequences.",
"Steinegger et al: HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinform 20(1), 473 (2019)",
"https://github.com/soedinglab/hh-suite",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"Pfam-A.full",
"The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models.",
"El-Gebali and Mistry et al: The Pfam protein families database in 2019. Nucleic Acids Res 47(D1), D427-D432 (2019)",
"https://pfam.xfam.org",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"Pfam-A.seed",
"The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models.",
"El-Gebali and Mistry et al: The Pfam protein families database in 2019. Nucleic Acids Res 47(D1), D427-D432 (2019)",
"https://pfam.xfam.org",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"Pfam-B",
"Pfam-B is a large automatically generated supplement to the Pfam database.",
"Sonnhammer et al: A new Pfam-B is released. Xfam Blog (2020)",
"https://xfam.wordpress.com/2020/06/30/a-new-pfam-b-is-released",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"CDD",
"Conserved Domain Database is a protein annotation resource consisting of well-annotated MSAs for ancient domains and full-length proteins.",
"Lu et al: CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res 48(D1), D265–D268 (2020)",
"https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"eggNOG",
"eggNOG is a hierarchical, functionally and phylogenetically annotated orthology resource",
"Huerta-Cepas et al: eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47(D1), D309–D314 (2019)",
"http://eggnog5.embl.de",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"VOGDB",
"VOGDB is a continously updated resource of Virus Orthologous Groups",
"Marz et al: Challenges in RNA virus bioinformatics. Bioinformatics 30, 1793–9 (2014)",
"https://vogdb.org",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"dbCAN2",
"dbCAN2 is a database of carbohydrate-active enzymes.",
"Zhang et al: dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46(W1), W95-W101 (2018)",
"http://bcb.unl.edu/dbCAN2",
false, Parameters::DBTYPE_HMM_PROFILE, databases_sh, databases_sh_len,
{ }
}, {
"SILVA",
"SILVA provides datasets of aligned small and large subunit ribosomal RNA sequences for all three domains of life.",
"Yilmaz et al: The SILVA and \"All-species Living Tree Project (LTP)\" taxonomic frameworks. Nucleic Acids Res 42(D1), D643-D648 (2014)",
"https://www.arb-silva.de",
true, Parameters::DBTYPE_NUCLEOTIDES, databases_sh, databases_sh_len,
{ { "SILVA_REL", "138" } }
}, {
"Resfinder",
"ResFinder is a database that captures antimicrobial resistance genes from whole-genome data sets.",
"Zankari et al: Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67(11), 2640-2644 (2012)",
"https://cge.cbs.dtu.dk/services/ResFinder",
false, Parameters::DBTYPE_NUCLEOTIDES, databases_sh, databases_sh_len,
{ }
}, {
"Kalamari",
"Kalamari contains over 250 genomes chosen to be representative of agents tracked by genome-based foodborne disease surveillance, common contaminants, and diverse phyla and bacterial genera.",
"Katz et al: Kraken with Kalamari: Contamination Detection. ASM Poster, 270 (2018)",
"https://github.com/lskatz/Kalamari",
true, Parameters::DBTYPE_NUCLEOTIDES, databases_sh, databases_sh_len,
{ }
},
};
29 changes: 29 additions & 0 deletions src/commons/DownloadDatabase.h
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//
// Created by Martin Steinegger on 10/1/21.
//

#ifndef MMSEQS_DOWNLOADDATABASE_H
#define MMSEQS_DOWNLOADDATABASE_H
#include <vector>
#include <string>


struct EnvironmentEntry {
const char* key;
const char* value;
};

struct DatabaseDownload {
const char *name;
const char *description;
const char *citation;
const char *url;
bool hasTaxonomy;
int dbType;
const unsigned char *script;
size_t scriptLength;
std::vector<EnvironmentEntry> environment;
};


#endif //MMSEQS_DOWNLOADDATABASE_H
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