:- set_prolog_flag(stack_limit, 2 000 000 000). :- 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). % also loads lib locations for locals below :- 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_dnt_times/3). :- lib(bio_db_add_infos/1). % bio_db_add_infos_to/2 :- lib(build_dnload_loc/3). :- lib(bio_db_source_url/3). :- lib(url_file_local_date_mirror/3). % fixme: this needs to be modernised, check the code in ../human and ../mouse std_chicken_maps_ense_defaults( [ db(ense), debug(true), debug_url(false), debug_fetch(true), ense_galg_file(call(ense_url_file)), iactive(true), org(chicken) ] ). /** std_chicken_maps_ense( +Opts ). Maps based on ensembl .gtf file. fixme: map_ense_gallus_ensg_symb.pl, 2nd arg contains "faf" and ENSG for some symbols, although the later might be margianlly useful ? Currently only gene symbols, but as per human it should be trivial to do sequences. * ense: the database abbv. Opts * db(Db=ense) source database * debug(Dbg=true) progress, informational 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) * iactive(Iact=true) whether the session is interactive, otherwise wget gets --no-verbose * ense_galg_file(Eile=call(ense_url_file)) the file name for the download (appended to Ufx@bio_db_source_base_url(gont_obo,Ufx))- or call that produces it * org(Org=chicken) organism == ?- std_chicken_maps_ense([]). ορέστης;build_repo/chicken% date ; pupsh std_chicken_maps_ense.pl ; date Tue 27 Dec 13:04:38 GMT 2022 % Building at: '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27' ... % ...Done Tue 27 Dec 13:09:40 GMT 2022 == @author nicos angelopoulos @version 0:1 2020/9/10 @tbd transcripts (see ../human/std_maps_ense.pl). @tbd use org_ense_dir (see human and mouse) */ std_chicken_maps_ense( Args ) :- std_chicken_maps_ense( galg, Args ), std_chicken_maps_ense( gg6a, Args ), std_chicken_maps_ense( gg7w, Args ). std_chicken_maps_ense( Tkn, Args ) :- Self = std_chicken_maps_ense, options_append( Self, Args, Opts ), bio_db_build_aliases( Opts ), build_dnload_loc( Self, DnDir, Opts ), SrcRnms = [ense_galg_file-url_file,debug_url-debug], bio_db_source_url( Url, SrcRnms, [org(Tkn)|Opts] ), url_file_local_date_mirror( Url, DnDir, [dnld_file(File),interface(wget)|Opts] ), debuc( Self, 'Dnload done, file is: ~p', File ), working_directory( Old, DnDir ), bio_db_dnt_times( File, DnDt, _DnEn ), debuc( by_unix ), @ gunzip(-k,-f,File), % os_un_zip( File, _, [keep(true),on_exists(skip),debug(true)] ), 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 ), debuc( Self, length, tg_rows/EnsTGRows ), debuc( Self, length, tl_rows/EnsTLRows ), at_con( [ense,Tkn,enst,'ensg.csv'], '_', EnsTGF ), % mtx( 'map_ense_gallus_enst_ensg.csv', EnsTGRows ), mtx( EnsTGF, EnsTGRows ), at_con( [ense,Tkn,enst,'chrl.csv'], '_', EnsTLF ), mtx( EnsTLF, EnsTLRows ), % mtx( 'map_ense_gallus_enst_chrl.csv', EnsTLRows ), ense_genes( Rows, Self, _EnsGMRows, EnsGSRows, EnsGCRows ), Lbls = [gtfRows,ensGM,ensGS,ensGC], % ERws = [Rows,EnsGMRows, EnsGSRows, EnsGCRows], ERws = [Rows, EnsGSRows, EnsGCRows], debuc( Self, length, Lbls/ERws ), % sort( EnsGSRows, EnsGSRowsSet ), at_con( [ense,Tkn,ensg,'symb.csv'], '_', EnsGSF ), % mtx( 'map_ense_gallus_ensg_symb.csv', EnsGSRowsSet ), mtx( EnsGSF, EnsGSRowsSet ), at_con( [ense,Tkn,ensg,'chrl.csv'], '_', EnsGLF ), mtx( EnsGLF, EnsGCRows ), % mtx( 'map_ense_gallus_ensg_chrl.csv', EnsGCRows ), Csvs = [ EnsTGF, % 'map_ense_gallus_enst_ensg.csv', EnsTLF, % 'map_ense_gallus_enst_chrl.csv', % % 'map_ense_gallus_ensg_mgim.csv', EnsGSF, % 'map_ense_gallus_ensg_symb.csv', EnsGLF % 'map_ense_gallus_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 Gene ID','Symbol'), row('Ensembl Gene 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 ), Cpts = call_options([org(gallus)]), map_list_options( link_to_bio_sub(ense), Pls, Cpts ), working_directory( _, Old ), debuc( Self, '...Done', true ). std_gallus_ense_gtf_file( galg, Found, MsGtfF ) :- findall( MsGtf-Amb-Rel, ( member(MsGtf,Found), at_con(['Gallus_gallus','bGalGal1',mat,broiler,GRChTkn,RelAtm,gtf,gz],'.',MsGtf), % atom_concat('GRCg',AmbAtm,GRChTkn), atom_concat('GRCg',Amb,GRChTkn), % atom_number(AmbAtm,Amb), atom_number(RelAtm,Rel), write( mar(MsGtf,Amb,Rel) ), nl ), MsGtfs ), ( MsGtfs = [MsGtfF-_Amb-_Rel] -> true ; throw( non_unique_auto_ided_ense_gtf_file(MsGtfs) ) ). std_gallus_ense_gtf_file( gg6a, Found, MsGtfF ) :- write( found(Found) ), nl, % Gallus_gallus_gca000002315v5.GRCg6a.108.gtf.gz findall( MsGtf-Amb-Rel, ( member(MsGtf,Found), at_con(['Gallus_gallus_gca000002315v5',GRChTkn,RelAtm,gtf,gz],'.',MsGtf), % atom_concat('GRCg',AmbAtm,GRChTkn), atom_concat('GRCg',Amb,GRChTkn), % atom_number(AmbAtm,Amb), atom_number(RelAtm,Rel), write( mar(MsGtf,Amb,Rel) ), nl ), MsGtfs ), ( MsGtfs = [MsGtfF-_Amb-_Rel] -> true ; throw( non_unique_auto_ided_ense_gtf_file(MsGtfs) ) ). 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, GSRows, [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,fail,Symb) -> GSRows = [row(EnsG,Symb)|TGSRows] ; GSRows = TGSRows ), !, ense_genes( Rows, Self, GMRows, 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 ). % fail if false ense_info_failure( false, _Key, _Lookup, false ). ense_chromosome( 'X' ) :- !. ense_chromosome( 'Y' ) :- !. ense_chromosome( N ) :- integer( N ), !.