:- set_prolog_flag(allow_dot_in_atom,false). :- set_prolog_flag(stack_limit, 8 000 000 000). :- use_module(library(csv)). % csv_read_file/2. :- use_module(library(lists)). % member/2. :- use_module(library(apply)). % maplist/4. % :- use_module(library(debug)). % /1,3. -> debug_call :- use_module(library(listing)). % portray_clause/2. :- use_module(library(readutil)). % read_line_to_codes/2. % if library(lib) is missing, install via pack_install(lib). % :- use_module( library(lib) ). % external code, lib knowns how to deal with these (will install if missing) :- lib(os_lib). :- lib(options). :- lib(debug_call). % debuc/1,3. :- lib(stoics_lib:map_list_options/3). % also sets lib alias to that dir :- ensure_loaded('../../lib/bio_db_build_aliases'). % /1. % local libs & sources :- lib(map_uniprot/4). :- lib(csv_ids_map/6). :- lib(link_to_bio_sub/3). :- lib(build_dnload_loc/3). :- lib(bio_db_dnt_times/3). :- lib(bio_db_add_infos/1). % bio_db_add_infos_to/2. :- lib(bio_db_source_url/3). :- lib(url_file_local_date_mirror/3). % use this if from outside europe: % unip_hs( 'ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz' ). % trem_hs( 'ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz' ). std_mouse_maps_unip_defaults( Defs ) :- Defs = [ db(unip), debug(true), debug_fetch(true), debug_url(false), org(mouse), unip_file_full('MOUSE_10090_idmapping.dat.gz'), unip_file_sele('MOUSE_10090_idmapping_selected.tab.gz') ]. /** std_mouse_maps_unip(+Opts). Create some uniprot maps. Opts * db(Db=unip) source database * debug(Dbg=true) informational, progress messages * debug_fetch(Ubg=true) whether to debug the fetching of the url (via url_file_local_date_mirror/3) * debug_url(Ubg=false) whether to debug the concatenation of the url (via bio_db_source_url/3) * org(Org=mouse) organism * unip_file_full(Uff='MOUSE_10090_idmapping.dat.gz' remote file name for Unip protein downloads (all proteins) * unip_file_sele(Ufs='MOUSE_10090_idmapping_selected.tab.gz') remote file name for Unip downloads (selected, annotated proteins- subset of Uff) == ?- maps_std_uniprot. ?- shell( 'wc -l uniprot_*' ). ορέστης;build_repo/mouse% date ; pupsh std_mouse_maps_unip.pl ; date Tue 27 Dec 16:05:52 GMT 2022 % Building at: '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27' % Loc: '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27/dnloads/unip' ... Tue 27 Dec 16:06:57 GMT 2022 ορέστης;unip/maps% date Tue 27 Dec 16:08:45 GMT 2022 ορέστης;unip/maps% pwd /usr/local/users/nicos/local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27/dnloads/unip/maps ορέστης;unip/maps% wc -l *_m* 67172 unip_musm_ensp_unip.pl 28758 unip_musm_gyno_unip.pl 80455 unip_musm_mgim_unip.pl 129676 unip_musm_trem_nucs.pl 32782 unip_musm_unip_ncbi.pl 83182 unip_musm_unip_symb.pl 422025 total == @author nicos angelopoulos @version 0.2 2015/4/27 @version 0.3 2023/9/25 use more local libs and control via options */ std_mouse_maps_unip( Args ) :- Self = std_mouse_maps_unip, options_append( Self, Args, Opts ), bio_db_build_aliases( Opts ), build_dnload_loc( Self, DnDir, Opts ), /* double check unip part works with the nucl part // 15.05.15 */ working_directory( Old, DnDir ), % unip_mouse( Url ), bio_db_source_url( Url, [debug_url-debug,unip_file_full-url_file], Opts ), % url_file( Url, UrlOpts = [debug(true),interface(wget),dnld_file(File)], options( debug_fetch(Fbg), Opts ), url_file_local_date_mirror( Url, DnDir, [debug(Fbg)|UrlOpts] ), os_make_path( maps, debug(true) ), debuc( Self, 'Dir location: ~p', DnDir ), Rev = [id_map('MOUSE_10090_idmapping.dat'),org(mouse),f_call(de_vers),interface(prolog),reverse(true)], map_uniprot( 'Ensembl_PRO', Csv, [EnspF], Rev ), Sem = [interface(prolog),f_call(de_semi('MGI')),reverse(true),id_map('MOUSE_10090_idmapping.dat'),org(mouse)], map_uniprot( 'MGI', Csv, [MgiF], Sem ), Ifc = [id_map('MOUSE_10090_idmapping.dat'),org(mouse),interface(prolog)], Rfc = [id_map('MOUSE_10090_idmapping.dat'),org(mouse),interface(prolog),reverse(true)], map_uniprot( 'GeneID', Csv, [EtzF], Ifc ), % map_uniprot( 'UniGene', Csv, [UniGF], Ifc ), map_uniprot( 'Gene_Name', Csv, [SymbF], Ifc ), map_uniprot( 'Gene_Synonym', Csv, [GynoF], Rfc ), % Files = [HgncF,FromHgncF,EtzF,UniGF,EnspF], % Files = [MgiF,EtzF,UniGF,EnspF,SymbF,GynoF], Files = [MgiF,EtzF,EnspF,SymbF,GynoF], link_to_bio_sub( unip, Files, [org(mouse),type(maps)] ), bio_db_dnt_times( File, SwDnDt, _SwDnEn ), SwOpts = [source(Url),datetime(SwDnDt)], bio_db_add_infos_to( [header(row('Ensembl_Protein','UniProt'))|SwOpts], 'maps/unip_musm_ensp_unip.pl' ), bio_db_add_infos_to( [header(row('Uni_Protein','Entrez_ID'))|SwOpts], 'maps/unip_musm_unip_ncbi.pl' ), bio_db_add_infos_to( [header(row('Uni_Protein','MGI'))|SwOpts], 'maps/unip_musm_mgim_unip.pl' ), % bio_db_add_infos_to( [header(row('Uni Protein','HGNC ID'))|SwOpts], 'maps/map_unip_mouse_unip_hgnc.pl' ), % Unigene has been discontinued %bio_db_add_infos_to( [header(row('Uni_Protein','Uni_Gene'))|SwOpts], 'maps/map_unip_mouse_unip_unig.pl' ), bio_db_add_infos_to( [header(row('Uni_Protein','Symbol'))|SwOpts], 'maps/unip_musm_unip_symb.pl' ), bio_db_add_infos_to( [header(row('Symbol','Uni_Protein'))|SwOpts], 'maps/unip_musm_gyno_unip.pl' ), working_directory( _, DnDir ), bio_db_source_url( TremUrl, [debug_url-debug,unip_file_sele-url_file], Opts ), % 15.05.14 adding support for treMBL, at least that 's what i think the selected file is all about TrUrlOpts = [debug(true),interface(wget),dnld_file(TrFile)], url_file_local_date_mirror( TremUrl, DnDir, TrUrlOpts ), bio_db_dnt_times( TrFile, TrDnDt, _TrDnEn ), os_make_path( maps, afresh(false) ), os_make_path( trembl, afresh(true) ), directory_file_path( _, TremFile, TremUrl ), % @ pwd(), directory_file_path( trembl, TremFile, TremTrg ), copy_file( TremFile, TremTrg ), working_directory( _, trembl ), file_name_extension( TremDatF, gz, TremFile ), atom_concat( 'gunzip ', TremFile, Gunzip ), debuc( Self, 'Gunzipping: ~p', TremFile ), shell( Gunzip ), csv_read_file( TremDatF, TremRows, [separator(0'\t)] ), debuc( Self, length, trem_rows/TremRows ), % 17/22 findall( unip_musm_trem_nucs(TremId,Nucs), ( member(TremRow,TremRows), arg(1,TremRow,TremId), \+ empty(TremId), arg(17,TremRow,NucsConcat), \+ empty(NucsConcat), atomic_list_concat(NucsList,'; ',NucsConcat), member(Nucs,NucsList) ), TNRows ), debuc( Self, length, tn_len/TNRows ), sort( TNRows, TNOrdRows ), open( '../maps/unip_musm_trem_nucs.pl', write, TNOut ), maplist( portray_clause(TNOut), TNOrdRows ), close( TNOut ), working_directory( _, '../maps' ), link_to_bio_sub( unip, 'unip_musm_trem_nucs.pl', [org(mouse),type(maps)] ), TrOpts = [source(TremUrl),datetime(TrDnDt),header(row('treMBLE_Protein','Nucleotide_Sequence'))], bio_db_add_infos_to( TrOpts, 'unip_musm_trem_nucs.pl' ), % run this manually, it is a biggie: % uniprot_sprot.dat is 2.9 G % std_map_usyn_unip, % working_directory( _, Old ). empty( '' ). /* std_map_usyn_unip :- open( '/media/nicos/lmtk3/downloads/uniprot_sprot.dat', read, In ), read_line_to_codes( In, Line ), sprot_synonym_rows( Line, In, SynRs ), debug_call( uniprot, length, syn_rows/SynRs ), close( In ), sort( SynRs, OrdRs ), unip_dnload( DnDir ), os_path( DnDir, maps, MapsD ), Opts = [prefix(unip),dir(MapsD)], csv_ids_map( _, usyn, unip, [row(usyn,unip)|OrdRs], MapF, Opts ), os_path( MapsD, MapF, AbsMapF ), % link_to_map_sub( unip, AbsMapF ). link_to_bio_sub( unip, AbsMapF, [org(mouse),type(maps)] ). */ sprot_synonym_rows( end_of_file, _In, [] ) :- !. sprot_synonym_rows( Line, In, SynRs ) :- atom_codes( Atom, Line ), ( atom_concat('AC ',SynsPsf,Atom) -> atom_concat(SynsAtom,';',SynsPsf), atomic_list_concat(Syns,'; ',SynsAtom), Syns = [Cannon|Ryns], sport_prot_synonym_rows( Ryns, Cannon, SynRs, TSynRs ) ; TSynRs = SynRs ), read_line_to_codes( In, Codes ), sprot_synonym_rows( Codes, In, TSynRs ). sport_prot_synonym_rows( [], _Cannon, SynRs, SynRs ). sport_prot_synonym_rows( [H|T], Cannon, [row(H,Cannon)|TSynRs], SynRs ) :- sport_prot_synonym_rows( T, Cannon, TSynRs, SynRs ). os_rm_rf( Dir ) :- exists_directory(Dir) -> delete_directory_and_contents(Dir), !. os_rm_rf( _Dir ). de_vers( Prv, Cln ) :- atomic_list_concat( [Cln,Ver], '.', Prv ), atom_number( Ver, _ ), !. de_vers( Cln, Cln ). de_semi( Pfx, AccPrv, Acc ) :- atomic_list_concat( [Pfx,AccAtm], ':', AccPrv ), atom_number( AccAtm, Acc ), !. de_semi( Pfx, AccPrv, _Acc ) :- write( de_semi_disaster(Pfx,AccPrv) ), nl, abort.