:- use_module(library(filesex)). % 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(by_unix). :- lib(options). :- lib(stoics_lib:at_con/3). :- lib(stoics_lib:portray_clauses/2). :- lib(stoics_lib:io_lines/2). % also sets lib alias that dir :- ensure_loaded(pack(bio_db/src/bio_db_build_aliases)). % /1 % local libs & sources :- lib(de_semi/3). :- lib(sep_split/3). :- lib(csv_ids_map/6). :- lib(link_to_bio_sub/2). :- lib(bio_db_dnt_times/3). :- lib(build_dnload_loc/3). :- lib(bio_db_add_infos/1). % bio_db_add_infos_to/2 :- lib(map_list_options/3). :- lib(bio_db_source_url/3). :- lib(url_file_local_date_mirror/3). true(_,_). std_chicken_maps_cgnc_defaults( Defs ) :- Defs = [ cgnc_file('standard'), dnld_file('cgnc_complete_set.txt'), db(cgnc), debug(true), debug_fetch(true), debug_url(false), download(true), iactive(true), org(chicken), sub(maps) ]. /** std_chicken_maps_cgnc( +Opts ). Create ID maps from CGNC's main download data file. Input is the tab delimited file containing all CGNC public data. The fields in the file are: CGNC ID, Entrez Gene ID, Ensembl Gene ID, gene symbol, gene name, gene synonym, curation status and last edit date. In the interest of completeness we create a map for each column based on CGNC ID (cgnc). Tokens * cgnc('CGNC id') chicken gene nomenclature consortium id * ncbi('Entrez') Ncbi/Entrez gene ids * ensg('Gene id') Ensembl gene ids * symb('gene symbol') Gene symobls * name('gene name') Gene, long, name. * syno('gene synonym') Gene synonym(s) - check syntax for multies * curs('curation status') Curation status (should be a factor) * edat('last edit date') should be a date data type Opts * cgnc_file(CgncF='cgnc_complete_set.txt') file for the CGNC download * db(Db=cgnc) source database * debug(Dbg=true) progress, informational messages * debug_fetch(Fbg=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) * download(Dn=true) set to false to skip downloading a fresh copy of the CGNC file(s) * iactive(Iact=true) whether the session is interactive, otherwise wget gets --no-verbose * org(Org=chicken) organism * sub(Dir=maps) sub-directory for creating the maps The download of CGNC is non standard as the full url is =|https://www.birdgenenames.org/downloads.jsp?file=standard|= == ?- std_chicken_maps_cgnc. ?- cd( '$HOME/.local/share/swi-prolog/pack/Downloads/bio_db-22.12.17/maps/cgnc' ). ?- shell( 'wc -l *' ). == @author nicos angelopoulos @version 0.1 2022/12/17, from hgnc @version 0.2 2025/09/25, url change @see http://www.birdgenenames.org/downloads.jsp?file=standard */ std_chicken_maps_cgnc :- std_chicken_maps_cgnc( [] ). std_chicken_maps_cgnc( Args ) :- Self = std_chicken_maps_cgnc, options_append( Self, Args, Opts ), bio_db_build_aliases( Opts ), options( download(Dnload), Opts ), build_dnload_loc( Self, DnDir, Opts ), bio_db_source_url( SrcUrl, [cgnc_file-url_file,debug_url-debug], Opts ), cgnc_download_file( Dnload, DnDir, Self, SrcUrl, DnlF, Opts ), working_directory( Old, DnDir ), os_ext( dnt, DnlF, DntF ), bio_db_dnt_times( DntF, DnDt, _DnEnd ), options( sub(SubDir), Opts ), make_directory_path( SubDir ), % 23.06.05, the cgnc file introduced a /9 (instead of /8 line in late May). % std_chicken_cgnc_mtx( CsvF, Mtx ), % 23.09.25, this seems fixed now mtx( DnlF, Mtx, sep(tab) ), debuc( Self, dims, mtx/Mtx ), StdO= [dir(SubDir),cnm_transform(cgnc_cname)|Opts], Cgnc = 'CGNC id', Symb = 'gene symbol', Ncbi = 'Entrez Gene id', Ensg = 'Ensembl Gene id', Name = 'gene name', Syno = 'gene synonym', Curs = 'curation status', Edat = 'last edit date', cgnc_std_map( Cgnc, Symb, DnlF, Mtx, Self, StdO, SrcUrl/DnDt, SymbF ), % cgnc_symb cgnc_std_map( Cgnc, Ncbi, DnlF, Mtx, Self, StdO, SrcUrl/DnDt, NcbiF ), % cgnc_ncbi cgnc_std_map( Cgnc, Ensg, DnlF, Mtx, Self, StdO, SrcUrl/DnDt, EnsgF ), % cgnc_ensg cgnc_std_map( Cgnc, Name, DnlF, Mtx, Self, StdO, SrcUrl/DnDt, NameF ), % cgnc_name cgnc_std_map( Cgnc, Syno, DnlF, Mtx, Self, StdO, SrcUrl/DnDt, SynoF ), % cgnc_syno cgnc_std_map( Cgnc, Curs, DnlF, Mtx, Self, StdO, SrcUrl/DnDt, CursF ), % cgnc_curs cgnc_std_map( Cgnc, Edat, DnlF, Mtx, Self, StdO, SrcUrl/DnDt, EdatF ), % cgnc_edat debuc( Self, 'doing links...', [] ), Files = [SymbF,NcbiF,EnsgF,NameF,SynoF,CursF,EdatF], % maplist( link_to_bio_sub(RelDir), Files ), options( db(Db), Opts ), map_list_options( link_to_bio_sub(Db), Files, call_options([org(chicken),type(maps)]) ), % file_name_extension( TxtF, gz, GzF ), % delete_file( TxtF ), working_directory( _, Old ). cgnc_std_map( Cid1, Cid2, DnlF, Csv, Self, StdO, SrcUrl/DnDt, OutF ) :- cgnc_std_column_to_value_call( Cid1, Call1 ), cgnc_std_column_to_value_call( Cid2, Call2 ), Opts = [to_value_1(Call1),to_value_2(Call2)|StdO], % debuc( std_maps_hgnc, 'doing file for columns: ~w, ~w', [Cid1, Cid2] ), csv_ids_map( DnlF, Cid1, Cid2, Csv, OutF, [source(SrcUrl),datetime(DnDt)|Opts] ), debuc( Self, 'deposited on: ~w (columns: ~w, ~w)', [OutF,Cid1,Cid2] ). cgnc_std_column_to_value_call('CGNC id', pos_integer). % check they are unique and present (key) % de_semi('CGNC') ). cgnc_std_column_to_value_call('Entrez Gene id', pos_integer). cgnc_std_column_to_value_call('Ensembl Gene id', not_empty). % fixme: prefixed cgnc_std_column_to_value_call('gene symbol', not_empty). cgnc_std_column_to_value_call('gene name', not_empty). cgnc_std_column_to_value_call('gene synonym', sep_split('|')). % fixme: check for multis cgnc_std_column_to_value_call('curation status', not_empty). cgnc_std_column_to_value_call('last edit date', not_empty). % fixme: a date cohese_ensebl_gene_id( Dom, _Subo, Gid ) :- Dom \== '', !, Gid = Dom. cohese_ensebl_gene_id( _Dom, Subo, Gid ) :- Subo \== '', !, Gid = Subo. cohese_ensebl_gene_id( _Dom, _Subo, '' ). cohese_gene_id( Dom, _Subo, Gid ) :- number( Dom ), Dom > 0, !, Gid = Dom. cohese_gene_id( _Dom, Subo, Gid ) :- number( Subo ), Subo > 0, !, Gid = Subo. cohese_gene_id( _Dom, _Subo, '' ). cgnc_cname( _, A, B ) :- cgnc_cname_known( A, B ), !. cgnc_cname( _, A, A ). % cmpl = complement = both currated by HGNC and supplied by respective database. % % CGNC id Entrez Gene id Ensembl Gene id gene symbol gene name gene synonym curation status last edit date cgnc_cname_known( 'CGNC id', cgnc ). cgnc_cname_known( 'Entrez Gene id', ncbi ). cgnc_cname_known( 'Ensembl Gene id', ensg ). cgnc_cname_known( 'gene symbol', symb ). cgnc_cname_known( 'gene name', name ). cgnc_cname_known( 'gene synonym', syno ). cgnc_cname_known( 'curation status', curs ). cgnc_cname_known( 'last edit date', edat ). % 23.06.05, the cgnc file introduced a /9 (instead of /8 line in late May). % in next version revert back to the mtx/3 call above std_chicken_cgnc_mtx( CsvF, Mtx ) :- mtx( CsvF, Csv, [match(false),sep(tab)] ), std_chicken_cgnc_mtx_fix( Csv, Mtx ). std_chicken_cgnc_mtx_fix( [], [] ). std_chicken_cgnc_mtx_fix( [H|Rs], [R|M] ) :- functor( H, _, Arity ), ( Arity =:= 8 -> R = H ; Arity =:= 9, H =.. [Func,89661,121109795,'','HSFX1','heat shock transcription factor','X1','','Approved','2023-05-23'], R =.. [Func,89661,121109795,'','HSFX1','heat shock transcription factor X1','','Approved','2023-05-23'] ), std_chicken_cgnc_mtx_fix( Rs, M ). cgnc_download_file( true, DnDir, Self, Url, DnlF, Opts ) :- % Url = 'http://birdgenenames.org/cgnc/downloads.jsp?file=standard', options( debug_fetch(Fbg), Opts ), url_file_local_date_mirror( Url, DnDir, [date(prefix),debug(Fbg),interface(wget)|Opts] ), memberchk( dnld_file(DnlF), Opts ), os_path( DnDir, DnlF, Dst ), cgnc_download_file_fix( Self, Dst ). cgnc_download_file( false, _DnDir, Self, _Url, DnlF, Opts ) :- memberchk( dnld_file(DnlF), Opts ), % options( cgnc_file(File), Opts ), debuc( Self, 'Asked not to download: ~p', [DnlF] ). % fixme: 25.9.25 commented this out, this has changed, and it should be set here. % Url = 'http://birdgenenames.org/cgnc/downloads.jsp?file=standard'. cgnc_download_file_fix( Self, Dst ) :- io_lines( Dst, Lines ), debuc( Self, length, cgnc_dnload/Lines ), Lines = [[13],BCs|Tines], atom_codes( B, BCs ), at_con( BParts, '\t', B ), % debuc( Self, enum, cgnc_2nd_line_parts/BParts ), % fixme: REPORT, there is "Ensembl Gene id missing on the header !" BParts = ['CGNC id','Entrez Gene id','gene symbol','gene name','gene synonym','curation status','last edit date'], BParts = [CGNC,Ncbi,Symb,Name,Syno,Curs,Edat], !, NewBParts = [CGNC,Ncbi,'Ensembl Gene id',Symb,Name,Syno,Curs,Edat], at_con( NewBParts, '\t', NewB ), atom_codes( NewB, NewBCs ), % maplist( cgnc_download_file_fix_line(Self), Tines, Nines ), % this is now fixed % io_lines( Dst, [NewBCs|Nines] ), io_lines( Dst, [NewBCs|Tines] ), debuc( Self, wrote, Dst ). cgnc_download_file_fix( Self, Dst ) :- debuc( Self, 'CGNC download seems in good order: ~p', [Dst] ). % There was an extra TAB, reported 25.09.25 % fixed on the same day cgnc_download_file_fix_line( Self, Line, Nine ) :- Line == `64661 100858424 ENSGALG00010024587 IL34 interleukin 34 interleukin 34 Interleukin-34|IL-34|chIL-34 Approved 2025-04-04`, !, debuc( Self, 'Fixing line: ~d', [64661] ), Nine = `64661 100858424 ENSGALG00010024587 IL34 interleukin 34 Interleukin-34|IL-34|chIL-34 Approved 2025-04-04`. cgnc_download_file_fix_line( _Self, Line, Line ).