:- set_prolog_flag(stack_limit, 4 000 000 000). :- use_module(library(lists)). :- use_module(library(apply)). :- use_module(library(lib)). :- lib(mtx). :- lib(os_lib). :- lib(by_unix). :- lib(debug_call). :- lib(stoics_lib:at_con/3). % sets libs and download aliases :- ensure_loaded(pack(bio_db/src/bio_db_build_aliases)). % /1 % local :- lib(csv_to_pl/2). :- lib(link_to_bio_sub/3). :- lib(bio_db_add_infos/1). % bio_db_add_infos_to/2 :- lib(bio_db_dnt_times/3). :- lib(build_dnload_loc/3). :- lib(bio_db_source_url/3). :- lib(url_file_local_date_mirror/3). std_maps_ense_defaults( Defs ) :- Defs = [ db(ense), debug(true), debug_url(false), debug_fetch(true), ense_musm_file(call(ense_url_file)), % make this common to all ense's org(mouse) ]. /** std_mouse_maps_ense( +Opts ). Maps based on ensembl .gtf file. Currently only gene symbols, but as per human it should be trivial to do sequences. * ense: the database abbv. Opts * db(ense) source database * debug(Dbg=true) informational, progress messages * debug_url(Ubg=false) whether to debug the concatenation of the url (via bio_db_source_url/2) * debug_fetch(Ubg=true) whether to debug the fetch of the URL * ense_homs_base(Eoms=ense_homs) Url or bio_db_source_base_url/2 token for download diretory * ense_homs_file(Eile=call(ense_homs_url_file)) the file name for the download (appended to Ufx@bio_db_source_base_url(gont_obo,Ufx))- or call that produces it * iactive(Iact=true) whether the session is interactive, otherwise wget gets --no-verbose * org(Org=mouse) organism * release(Release) release number == date ; pupsh std_mouse_maps_ense.pl ; date Tue 27 Dec 14:58:14 GMT 2022 % Building at: '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27' ... % Symbolic linking, '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27/dnloads/ense/maps/ense_musm_ensg_symb.pl', to '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27/data/musm/maps/ense/ense_musm_ensg_symb.pl' % ...Done Tue 27 Dec 15:02:55 GMT 2022 ορέστης;ense/maps% date Tue 27 Dec 15:05:38 GMT 2022 ορέστης;ense/maps% pwd /usr/local/users/nicos/local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27/dnloads/ense/maps ορέστης;ense/maps% wc -l *_m* 56987 ense_musm_ensg_chrl.pl 55441 ense_musm_ensg_mgim.pl 56987 ense_musm_ensg_symb.pl 149393 ense_musm_enst_chrl.pl 149393 ense_musm_enst_ensg.pl 468201 total == @author nicos angelopoulos @version 0:1 2020/9/10 @tbd transcripts (see std_maps_ense.pl). */ std_mouse_maps_ense( Args ) :- Self = std_maps_ense, options_append( Self, Args, Opts ), bio_db_build_aliases( Opts ), ensure_loaded(mgim:bio_db_build_downloads('mgim/maps/mgim_musm_mgim_symb')), ensure_loaded(mgim:bio_db_build_downloads('mgim/maps/mgim_musm_msyn_mgim')), build_dnload_loc( Self, DnDir, Opts ), debuc( Self, 'Downloads dir for ense: ~p', DnDir ), SrcRnms = [ense_musm_file-url_file,debug_url-debug], bio_db_source_url( Url, SrcRnms, Opts ), url_file_local_date_mirror( Url, DnDir, [dnld_file(File)|Opts] ), debuc( Self, 'Dnload done, file is: ~p', File ), working_directory( Old, DnDir ), bio_db_dnt_times( File, DnDt, _DnEn ), debuc( by_unix ), % os_un_zip( File, _, [keep(true),on_exists(skip),debug(true)] ), @ gunzip( -k, -f, File ), os_ext( gz, Stem, File ), debuc( Self, 'Reading from: ~p', [Stem] ), mtx( Stem, Rows, [sep(tab),csv_read(skip_header('#'))] ), debuc( Self, length, rows/Rows ), % ense_genes( Rows, EnsGHRows, EnsGSRows, EnsGCRows ), ense_transcripts( Rows, EnsTGRows, EnsTLRows ), mtx( 'ense_musm_enst_ensg.csv', EnsTGRows ), mtx( 'ense_musm_enst_chrl.csv', EnsTLRows ), ense_genes( Rows, Self, EnsGMRows, EnsGSRows, EnsGCRows ), Lbls = [gtfRows,ensGM,ensGS,ensGC], ERws = [Rows,EnsGMRows, EnsGSRows, EnsGCRows], debuc( Self, length, Lbls/ERws ), % % mtx( 'map_ense_mouse_ensg_msgi.csv', EnsGHRows ), % sort( EnsGCRows, EnsGCRowsSet ), sort( EnsGSRows, EnsGSRowsSet ), sort( EnsGMRows, EnsGMRowsSet ), Sets = [EnsGMRowsSet,EnsGSRowsSet], debuc( Self, length, [gmSet,gsSet,gcSet]/Sets ), /* fixme: create a fast version, this is only for printing ... findall( Symb, ( mgim:map_mgim_mouse_mgim_symb(_,Symb), \+ memberchk( row(_,Symb), EnsGSRowsSet) % debuc(Self,'MGIM symbol, not in Ensembl: ~w', Symb ) ), NonMgimSymbs ), findall( Symb, mgim:map_mgim_mouse_mgim_symb(_,Symb), AllSymbs ), debuc( Self, length, [mgim_symb_not_in_ense,total]/[NonMgimSymbs,AllSymbs] ), */ mtx( 'ense_musm_ensg_mgim.csv', EnsGMRowsSet ), mtx( 'ense_musm_ensg_symb.csv', EnsGSRowsSet ), mtx( 'ense_musm_ensg_chrl.csv', EnsGCRows ), Csvs = [ 'ense_musm_enst_ensg.csv', 'ense_musm_enst_chrl.csv', 'ense_musm_ensg_mgim.csv', 'ense_musm_ensg_symb.csv', 'ense_musm_ensg_chrl.csv' ], debuc( Self, 'mapping: ~w', [Csvs] ), maplist( csv_to_pl(Self), Csvs ), maplist( new_ext(pl), Csvs, Pls ), AddOpts = [source(Url),datetime(DnDt)], Headers = [ row('Ensembl Transcript','Ensembl Gene'), row('Ensembl Transcript','Chromosome', 'Start', 'End', 'Direction'), row('Ensembl ID','MGIM ID'), row('Ensembl ID','Symbol'), row('Ensembl ID','Chromosome', 'Start', 'End', 'Direction') ], findall( PlF, ( nth1(N,Pls,PlF), nth1(N,Headers,Header), debuc( Self, 'ingoing prolog file: ~p', PlF ), debuc( Self, '...with header: ~w and options: ~w', [Header,AddOpts] ), bio_db_add_infos_to([header(Header)|AddOpts], PlF) ), _PlFs ), os_make_path( maps ), maplist( mv_to_sub(maps), Pls ), @ rm( -f, Stem ), working_directory( _, maps ), link_to_bio_sub( ense, Pls, [org(mouse),type(maps)] ), working_directory( _, Old ), debuc( Self, '...Done', true ). mv_to_sub( Sub, File ) :- os_path( Sub, File, Rel ), rename_file( File, Rel ). new_ext( New, File, NewFile ) :- os_ext( _Old, New, File, NewFile ). ense_genes( [], _Self, [], [], [] ). ense_genes( [RowG|Rows], Self, GMRows, [GSRow|TGSRows], [EnsGC|GCRows] ) :- RowG = row(ChrG,_Db,gene,SrtG,EndG,_,DirG,_,InfoG), EnsGC= row(EnsG,ChrG,SrtG,EndG,DirG), ense_info( gene_id, InfoG, EnsG ), ense_info( gene_name, InfoG, def(EnsG), Syno ), % ense_gene_hgnc( EnsG, EnsN, GHRows, GSRows, TGHRows, TGSRows ), % fixme: check Symb is an mgim symbol ? ( mgim:mgim_musm_mgim_symb(SynoGim,Syno) -> Syno = Symb, GMRows = [row(EnsG,SynoGim)|TGMRows] ; ( ( mgim:mgim_musm_msyn_mgim(Syno,Mgim), mgim:mgim_musm_mgim_symb(Mgim,Symb) ) -> GMRows = [row(EnsG,Mgim)|TGMRows] ; GMRows = TGMRows, Syno = Symb, debuc( std_maps_ense(details), 'Not an MGIM symbol: ~w', Syno ) ) ), GSRow = row(EnsG,Symb), !, ense_genes( Rows, Self, TGMRows, TGSRows, GCRows ). ense_genes( [RowG|Rows], _Self, _, _, _ ) :- RowG = row(_ChrG,_Db,gene,_SrtG,_EndG,_,_DirG,_,_InfoG), !, length( Rows, Len ), throw( tripped_on_gene_row(RowG,Len) ). ense_genes( [_RowG|Rows], Self, GMRows, GSRows, GCRows ) :- ense_genes( Rows, Self, GMRows, GSRows, GCRows ). ense_transcripts( [], [], [] ). ense_transcripts( [RowT|Rows], [EnsTG|TGRows], [EnsTL|TLRows] ) :- RowT = row(ChrT,_Db,transcript,SrtT,EndT,_,DirT,_,InfoT), % findall( row(EnsT,EnsG)-row(EnsT,ChrT,SrtT,EndT,DirT), ( )). ense_info( transcript_id, InfoT, EnsT ), ense_info( gene_id, InfoT, EnsG ), ense_chromosome( ChrT ), !, EnsTG = row(EnsT,EnsG), EnsTL = row(EnsT,ChrT,SrtT,EndT,DirT), ense_transcripts( Rows, TGRows, TLRows ). ense_transcripts( [RowT|Rows], _, _ ) :- RowT = row(ChrT,_Db,transcript,_SrtT,_EndT,_,_DirT,_,_InfoT), ense_chromosome( ChrT ), !, length( Rows, Len ), throw( tripped_on_transcript_row(RowT,Len) ). ense_transcripts( [_RowT|Rows], TGRows, TLRows ) :- ense_transcripts( Rows, TGRows, TLRows ). ense_info( Key, Lookup, Value ) :- ense_info( Key, Lookup, true, Value ). ense_info( Key, Lookup, _Strict, Value ) :- atomic_list_concat( Parts, '"; ', Lookup ), atom_concat( Key, ' "', Left ), member( Part, Parts ), atom_concat( Left, Value, Part ), !. ense_info( Key, Lookup, Strict, Value ) :- ense_info_failure( Strict, Key, Lookup, Value ). ense_info_failure( true, Key, Lookup, _ ) :- throw( lookup_failure(Key,Lookup) ). ense_info_failure( def(Def), _Key, _Lookup, Def ). ense_info_failure( false, _Key, _Lookup, false ). ense_chromosome( 'X' ) :- !. ense_chromosome( 'Y' ) :- !. ense_chromosome( N ) :- integer( N ), !.