:- set_prolog_flag(stack_limit, 80 000 000 000). :- use_module(library(csv)). % csv_read_file/3. :- use_module(library(filesex)). % directory_file_path/3, copy_file/2. :- use_module(library(apply)). % maplist/2. :- use_module(library(lists)). % member/2. :- 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(by_unix). % @/1. :- lib(os_lib). :- lib(options). :- lib(debug_call).% /3. % sets libs and download aliases :- ensure_loaded(pack(bio_db/src/bio_db_build_aliases)). % /1 % local libs :- lib(map_uniprot/4). :- lib(csv_ids_map/6). :- lib(link_to_bio_sub/2). :- 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). std_maps_unip_defaults( Defs ) :- Defs = [ db(unip), debug(true), debug_url(false), debug_fetch(true), iactive(true), org(human), unip_file_full('HUMAN_9606_idmapping.dat.gz'), unip_file_sele('HUMAN_9606_idmapping_selected.tab.gz') ]. %% maps_std_unip(+Opts). % % Create 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) % * iactive(Iact=true) % whether the session is interactive, otherwise wget gets --no-verbose % * unip_file_full(UnipFF='HUMAN_9606_idmapping.dat.gz') % the file name for the obo download % * unip_file_sele(UnipFF='HUMAN_9606_idmapping.dat.gz') % the file name for the selected ids mapping download (stricter than the above) % %== % ?- maps_std_uniprot. % ?- shell( 'wc -l uniprot_*' ). %== % % @author nicos angelopoulos % @version 0.2 2015/4/27 % @tbd use hgnc as template to download from % std_maps_unip( Args ) :- Self = std_maps_unip, options_append( Self, Args, Opts ), bio_db_build_aliases( Opts ), build_dnload_loc( Self, DnDir, Opts ), working_directory( Old, DnDir ), bio_db_source_url( Url, [debug_url-debug,unip_file_full-url_file], Opts ), options( debug_fetch(Fbg), Opts ), url_file_local_date_mirror( Url, DnDir, [dnld_file(Bname),debug(Fbg)|Opts] ), os_make_path( maps, debug(true) ), % debuc( Self, 'Dir location: ~p', DnDir ), Rev = [interface(prolog),reverse(true)], map_uniprot( 'Ensembl_PRO', Csv, [EnspF], Rev ), % Fgnc = [interface(prolog),f_call(de_semi('HGNC'))], map_uniprot( 'HGNC', Csv, [FromHgncF], Fgnc ), % Sem = [interface(prolog),f_call(de_semi('HGNC')),reverse(true)], map_uniprot( 'HGNC', Csv, [HgncF], Sem ), % Ifc = interface(prolog), map_uniprot( 'GeneID', Csv, [EtzF], Ifc ), % map_uniprot( 'UniGene', Csv, :- use_module(library(filesex)).[UniGF], Ifc ), Files = [HgncF,FromHgncF,EtzF,EnspF], maplist( link_to_bio_sub(unip), Files ), % bio_db_dnt_times( Bname, SwDnDt, _SwDnEn ), SwOpts = [source(Url),datetime(SwDnDt)], bio_db_add_infos_to( [header(row('Ensembl Protein','Uni Protein'))|SwOpts], 'maps/unip_homs_ensp_unip.pl' ), bio_db_add_infos_to( [header(row('Uni Protein','Entrez ID'))|SwOpts], 'maps/unip_homs_unip_entz.pl' ), bio_db_add_infos_to( [header(row('Uni Protein','HGNC ID'))|SwOpts], 'maps/unip_homs_unip_hgnc.pl' ), bio_db_source_url( TremUrl, [debug_url-debug,unip_file_sele-url_file], Opts ), TrUrlOpts = [debug(true),interface(wget),dnld_file(TremFile)|Opts], url_file_local_date_mirror( TremUrl, DnDir, [debug(Fbg)|TrUrlOpts] ), bio_db_dnt_times( TremFile, TrDnDt, _TrDnEn ), debuc( Self, 'File: ~w, dnt_start: ~w', [TremFile,TrDnDt] ), os_make_path( maps, afresh(false) ), os_make_path( trembl, afresh(true) ), debuc( Self, 'File: ~w, Url: ~w', [TremFile,TremUrl] ), debuc( Self, pwd, false ), 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/TremRows ), % findall( unip_homs_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/TNRows ), sort( TNRows, TNOrdRows ), open( '../maps/unip_homs_trem_nucs.pl', write, TNOut ), maplist( portray_clause(TNOut), TNOrdRows ), close( TNOut ), working_directory( _, '../maps' ), @ rm( -rf, '../trembl' ), % fixme: untested in real run..... link_to_bio_sub(unip, 'unip_homs_trem_nucs.pl' ), TrOpts = [source(TremUrl),datetime(TrDnDt),header(row('treMBLE Protein','Nucleotide Sequence'))], bio_db_add_infos_to( TrOpts, 'unip_homs_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 ), debuc( 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_bio_sub( unip, AbsMapF ). */ 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 ). /* delete me os_rm_rf( Dir ) :- exists_directory(Dir) -> delete_directory_and_contents(Dir), !. os_rm_rf( _Dir ). */ 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.