:- use_module( library(lib) ). :- lib(csv). % ! :- lib(os_lib). :- lib(by_unix). :- lib(debug_call). :- lib( stoics_lib:en_list/2 ). map_uniprot_defaults( [ db(unip), destination(maps), ext([]), f_call(=), id_map('HUMAN_9606_idmapping.dat'), interface(prolog), reverse(false) ] ). % :- lib( options_append/3 ). % :- lib( gunzip/2 ). % :- lib( true/2 ). :- lib(map_predicate_name/4). % see above,... :- lib( map_predicate_name_stem/3 ). :- lib( csv_ids_map/6 ). % :- lib( csv_ids_interface_map/9 ). :- debuc(uniprot). /** map_uniprot( +Foreign ). map_uniprot( +Foreign, +Opts ). map_uniprot( +Foreign, ?UniprotCsv, -Written, +Opts ). Create a map file from Uniprot identifiers to a Foreign table. UniprotCsv allows multiple calls to map_uniprot/3 to utilise the read Csv. Written is the list of all files written on. Options * id_map('HUMAN_9606_idmapping.dat.gz') file- only used if UniprotCsv is an unbound variable * f_call(=) call to transform input Foreign accession to storable accession * interface(prolog) which interfaces to save- a list if more than one required (sqlite,prolog) * predicate(Predicate) predicate name, default is uniprot_ * stem(Stem) stem of the output file(s) (defaults to Predicate * destination('.') destination directory * ext([]) default depends on Interface (sqlite-> sqlite, prolog -> pl) (can be a list if Interface is one) * reverse(Rev=false) reverse the order of 'Protein' and 'Foreign' == ?- uniprot_sqlite_map( 'GeneID' ). == @author nicos angelopoulos @version 0.1 2014/7/2 @see map_predicate_name/4 */ map_uniprot( Foreign ) :- map_uniprot( Foreign, _, _, [] ). map_uniprot( Foreign, Opts ) :- map_uniprot( Foreign, _, _, Opts ). map_uniprot( Foreign, Uniprot, Fouts, Args ) :- options_append( map_uniprot, Args, Opts ), memberchk( id_map(UniprotFile), Opts ), memberchk( f_call(Fcall), Opts ), uniprot_load( UniprotFile, Uniprot ), findall( row(Prot,FAcc), ( member(row(Prot,Foreign,FAccPrv),Uniprot), call( Fcall, FAccPrv, FAcc ) ), PFRows ), debuc( uniprot, length, pf_rows/PFRows ), memberchk( interface(FcePrv), Opts ), en_list( FcePrv, Fces ), memberchk( destination(Dst), Opts ), memberchk( reverse(Rev), Opts ), reverse_column_names( Rev, uniprot, Foreign, Cnm1, Cnm2 ), maplist( uniprot_cname, [Cnm1,Cnm2], [Tnm1,Tnm2] ), map_predicate_name( Tnm1, Tnm2, Pname, Opts ), map_predicate_name_stem( Pname, Stem, Opts ), output_extensions( Opts, Fces, FExtsPrv ), sort( FExtsPrv, FExts ), maplist( map_uniprot_interface(Foreign,Pname,Stem,Dst,PFRows,Rev), FExts, Fouts ). map_uniprot_interface( Foreign, Pname, Stem, Dst, PFRows, Rev, Fce-Ext, Fout ) :- map_uniprot_save( Fce, Ext, Foreign, Pname, Stem, Dst, PFRows, Rev, Fout ). uniprot_load( _Partial, Rows ) :- ground( Rows ), !. uniprot_load( Partial, Rows ) :- member( Ext, ['',dat,'dat.gz','gz'] ), file_name_extension( Partial, Ext, File ), exists_file( File ), !, uniprot_load_file( File, Rows ). uniprot_load( Partial, Rows ) :- absolute_file_name( bio_db_downloads(unip), UnipD ), working_directory( Old, UnipD ), Old \== UnipD, !, uniprot_load( Partial, Rows ), working_directory( _, Old ). uniprot_load( Partial, _Rows ) :- throw( could_not_locate_uniprot_id_mappings_file(Partial) ). % fixme uniprot_load_file( File, Rows ) :- file_name_extension( Stem, gz, File ), !, @ gunzip( --keep, --force, File ), \+ file_name_extension( _, gz, Stem ), % just in case uniprot_load_file( Stem, Rows ), delete_file( Stem ). uniprot_load_file( File, Rows ) :- debuc( uniprot, 'Reading UniProt source at:~p', File ), csv_read_file( File, Rows, [separator(0'\t)] ). map_uniprot_save( sqlite, Ext, Foreign, Pname, Stem, Dst, PFRows, Rev, File ) :- % fixme: Rev not implemented here ( Rev == false -> true; throw( unimplemented_rev_flag_in_sqlite_interface(Rev) ) ), use_module( library(prosqlite) ), use_module( library(db_facts) ), os_dir_stem_ext( Dst, Stem, Ext, File ), sqlite_connect( File, uniprot, exists(false) ), debuc( uniprot, 'Opened sqlite connection to: ~p', File ), Create =.. [Pname,uniprot+text,Foreign+text], db_create( uniprot, Create ), debuc( uniprot, time(start), 'write on file' ), findall( _, (member(row(UniP,Fid),PFRows),Assert=..[Pname,UniP,Fid],db_assert(Assert)), _ ), debuc( uniprot, time(finish), 'write on file' ), sqlite_disconnect( uniprot ). map_uniprot_save( prolog, Ext, Foreign, Pname, Stem, Dst, PFRows, Rev, File ) :- os_dir_stem_ext( Dst, Stem, Ext, File ), os_dir_stem_ext( Dst, Stem, '', DstStem ), debuc( uniprot, 'Opened prolog output to: ~p', File ), findall( U, member(row(U,_),PFRows), Us ), findall( N, member(row(_,N),PFRows), Ns ), IfcOpts = [to_value_1(=),to_value_2(=)], reverse_columns( Rev, 'Uniprot', Foreign, Us, Ns, Cnm1, Cnm2, Clm1, Clm2 ), csv_ids_interface_map( prolog, Pname, DstStem, Cnm1, Cnm2, Clm1, Clm2, _PlFile, IfcOpts ). reverse_column_names( false, Cnm1, Cnm2, Cnm1, Cnm2 ). reverse_column_names( true, Cnm1, Cnm2, Cnm2, Cnm1 ). reverse_columns( false, Cnm1, Cnm2, Clm1, Clm2, Cnm1, Cnm2, Clm1, Clm2 ). reverse_columns( true, Cnm2, Cnm1, Clm2, Clm1, Cnm1, Cnm2, Clm1, Clm2 ). map_uniprot_save( pl, Ext, Foreign, Pname, Stem, Dst, PFRows, File ) :- map_uniprot_save( prolog, Ext, Foreign, Pname, Stem, Dst, PFRows, File ). output_extensions( Opts, Fces, Fexts ) :- memberchk( ext(ExtPrv), Opts ), en_list( ExtPrv, Exts ), findall( Fce-Ext, (nth1(N,Fces,Fce),nth_interface_ext(N,Exts,Fce,Ext)), Fexts ). nth_interface_ext( N, Exts, _Fce, Ext ) :- nth1( N, Exts, Ext ), !. nth_interface_ext( _N, _Exts, Fce, Ext ) :- interface_extension( Fce, Ext ). interface_extension( sqlite, sqlite ). interface_extension( prolog, pl ). interface_extension( pl, pl ). uniprot_cname( A, B ) :- debuc( uniprot, 'trying ~w', uniprot_cname_known(A, B) ), uniprot_cname_known( A, B ), !. uniprot_cname( A, A ). uniprot_cname_known( 'Ensembl_PRO', ensp ). uniprot_cname_known( 'uniprot', unip ). uniprot_cname_known( 'HGNC', hgnc ). uniprot_cname_known( 'GeneID', ncbi ). uniprot_cname_known( 'UniGene', unig ). % mouse uniprot_cname_known( 'MGI', mgim ). uniprot_cname_known( 'Gene_Name', symb ). uniprot_cname_known( 'Gene_Synonym', gyno ). % chicken uniprot_cname_known( 'STRING', strp ).