:- 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. % also sets lib alias to that dir :- ensure_loaded('../../lib/bio_db_build_aliases'). %/1. % local libs & sources :- lib(csv_ids_map/6). :- lib(link_to_bio_sub/2). :- lib(bio_db_dnt_times/3). :- lib(url_file_local_date_mirror/3). :- lib(bio_db_add_infos/1). % bio_db_add_infos_to/2 :- lib(map_uniprot/4). % :- debuc(uniprot). % :- debuc(link_to_map_sub). unip_hs( 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz' ). trem_hs( 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz' ). % 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' ). unip_dnload( Loc ) :- absolute_file_name( bio_db_build_downloads(unip), Loc ), debuc( uniprot, 'Loc: ~p', Loc ), os_make_path( Loc, debug(true) ). std_maps_unip_defaults( debug(true) ). %% maps_std_unip(Opts). % % Create uniprot maps. % %Opts % * debug(Dbg=true) % informational messages %== % ?- maps_std_uniprot. % ?- shell( 'wc -l uniprot_*' ). %== % % @author nicos angelopoulos % @version 0.2 2015/4/27 % @tbd use hgnc as template to download from % @tbd ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ % std_maps_unip( Args ) :- Self = std_maps_unip, options_append( Self, Args, Opts ), bio_db_build_aliases( Opts ), unip_dnload( DnDir ), % /* double check unip part works with the nucl part // 15.05.15 */ working_directory( Old, DnDir ), unip_hs( Url ), % url_file( Url, UrlOpts = [debug(true),interface(wget),file(File)], url_file_local_date_mirror( Url, DnDir, UrlOpts ), % cd( bio_dn_root(uniprot) ), % os_rm_rf( maps ), % don't do that, mouse puts stuff there too 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,UniGF,EnspF], Files = [HgncF,FromHgncF,EtzF,EnspF], % working_directory( _, maps ), maplist( link_to_bio_sub(unip), Files ), bio_db_dnt_times( File, 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_add_infos_to( [header(row('Uni Protein','Uni Gene'))|SwOpts], 'maps/map_unip_unip_unig.pl' ), % working_directory( _, DnDir ), trem_hs( TremUrl ), % 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),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 ), 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 ), % 17/22 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( _, '..' ), 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.