:- set_prolog_flag(stack_limit, 80 000 000 000).
:- use_module(library(csv)). % csv_read_file/3.
:- use_module(library(apply)). % maplist/2.
:- use_module(library(lists)). % member/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(mtx).
:- lib(os_lib).
:- lib(by_unix).
:- lib(stoics_lib:map_succ_list/3).
% also sets lib alias to that dir
:- ensure_loaded('../../lib/bio_db_build_aliases'). % /1.
% load necessary data that has already been generated
% :- ensure_loaded( hgnc:bio_db_build_downloads('hgnc/maps/map_hgnc_symb_hgnc') ).
% local libs & sources
% :- lib(go_id/2). -> go_obo_id/2 from below
:- lib(go_obo/2). %
:- 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).
% :- debuc(std_maps_go).
std_maps_gont_defaults( Defs ) :-
Defs = [ db(gont),
debug(true),
debug_fetch(true),
debug_url(false),
goa_base(gont_goa),
goa_file('goa_human.gaf.gz'),
iactive(true),
obo_base(gont_obo),
obo_file('go.obo'),
org(human)
].
% std_maps_gont( Opts ).
%
% Set up some standard maps for gene ontology (GO, gont) data.
%
% Source: http://geneontology.org/gene-associations/gene_association.goa_human.gz
%
% Currrently this sets ups
% * map_gont_gont_symb( GOTERM, Symb ).
% * map_gont_symb_gont( Symb, GOTERM ).
%
% TermGz = 'go_daily-termdb-tables.tar.gz',
% * map_gont_gont_gonm( GOTERM, GONM ).
%
% Opts
% * db(Db=gont)
% source database
% * debug(Dbg=true)
% informational, progress messages
% * debug_fetch(Fbg=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)
% * goa_base(GoaB=gont_goa)
% bio_db_source_base_url/2, token or url to download from
% * goa_file(GoaF='goa_human.gaf.gz')
% the file name for the download (appended to Ufx@bio_db_source_base_url(gont_goa,Ufx))
% * iactive(Iact=true)
% whether the session is interactive, otherwise wget gets --no-verbose
% * obo_base(OboB=gont_obo)
% the url base for the obo download
% * obo_file(OboF='go.obo')
% the file name for the obo download
%
% @author nicos angelopoulos
% @version 0.1 2015/3/26
% @version 0.2 2023/9/22, moved download location to options
% @see bio_db_source_base_url/2, bio_db_source_url/3.
%
std_maps_gont( Args ) :-
Self = std_maps_gont,
options_append( Self, Args, Opts ),
bio_db_build_aliases( Opts ),
% DnDir = '/usr/local/users/nicos/work/db/data/go',
% load necessary data that has already been generated
ensure_loaded( hgnc:bio_db_build_downloads('hgnc/maps/hgnc_homs_symb_hgnc') ),
build_dnload_loc( Self, DnDir, Opts ),
working_directory( Here, DnDir ),
SrcRnms = [debug_url-debug,goa_base-url_base,goa_file-url_file],
bio_db_source_url( Url, SrcRnms, Opts ),
options( debug_fetch(Fbg), Opts ),
url_file_local_date_mirror( Url, DnDir, [dnld_file(GoaF),debug(Fbg)|Opts] ),
@ gunzip( --force, -k, GoaF ),
file_name_extension( GoaHs, gz, GoaF ),
% mtx( 'gene_association.goa_human.tsv', Mtx ),
% mtx( GoaHs, Mtx, csv_read(sep=0'\t) ),
csv_read_file( GoaHs, MtxPrv, [separator(0'\t),match_arity(false),convert(false)] ),
clense_goa_hs( MtxPrv, Mtx ),
debuc( Self, 'loaded data...', true ),
make_directory_path( maps ),
gaf_gont_symb( Mtx, Self, NonSymbs, MultSymbs, NewRows ),
% fixme: make the messages more informative
debuc( Self, length, [non_symboled,multi_symboled]/[NonSymbs,MultSymbs] ),
sort( NewRows, OrdRows ),
mtx( 'maps/gont_homs_gont_symb.csv', OrdRows ),
GSopts = [predicate_name(gont_homs_gont_symb)],
mtx_prolog( OrdRows, 'maps/gont_homs_gont_symb.pl', GSopts ),
working_directory( AtHere, AtHere ),
debuc( Self, 'Currently at: ~p', AtHere ),
% bio_db_dnt_times( 'gene_association.goa_human.gz', UrlDntSt, _DntEnd ),
bio_db_dnt_times( GoaF, UrlDntSt, _DntEnd ),
AddOpts = [source(Url),datetime(UrlDntSt)],
bio_db_add_infos_to( [header(row('GO Term','Evidence','HGNC Symbol'))|AddOpts], 'maps/gont_homs_gont_symb.pl' ),
findall( row(Symb,Evid,Gont), member(row(Gont,Evid,Symb),OrdRows), SGRows ),
sort( SGRows, OrdSGRows ),
SGopts = [predicate_name(gont_homs_symb_gont)],
mtx_prolog( OrdSGRows, 'maps/gont_homs_symb_gont.pl', SGopts ),
bio_db_add_infos_to( [header(row('HGNC Symbol','Evidence','GO Term'))|AddOpts], 'maps/gont_homs_symb_gont.pl' ),
debuc( Self, 'Building term to name map', true ),
OboRnms = [debug_fetch-debug,obo_base-url_base,obo_file-url_file],
bio_db_source_url( OboUrl, OboRnms, Opts ),
absolute_file_name( bio_db_build_downloads(gont), DnDir ),
url_file_local_date_mirror( OboUrl, DnDir, [dnld_file(OboF),debug(Fbg)|Opts] ),
debuc( Self, 'Dnload done: ~w', [DnDir] ),
go_obo( OboF, GoObo),
go_obo_non_obs( GoObo, GoOboCurr ),
GoOboCurr = obo(_,OboTerms),
findall( gont_homs_gont_gonm(Gont,Gonm), member(obo_term(Gont,Gonm,_Nspc,_Obs,_Props),OboTerms), GontGonms ),
sort( GontGonms, OrdGontGonms ),
bio_db_dnt_times( 'go.obo', DnDt, _DnEnd ),
portray_clauses( OrdGontGonms, file('maps/gont_homs_gont_gonm.pl') ),
InfoOpts = [header(row('GO Term','GO Name')),source(OboUrl),datetime(DnDt)],
bio_db_add_infos_to( InfoOpts, 'maps/gont_homs_gont_gonm.pl' ),
working_directory( First, maps ),
OutFs = ['gont_homs_gont_symb.pl','gont_homs_symb_gont.pl','gont_homs_gont_gonm.pl'],
maplist( link_to_bio_sub(gont), OutFs ),
working_directory( _, First ),
delete_file( GoaHs ),
% delete_file( TermTar ),
working_directory( _, Here ).
% fixme: parse Go through grammar
gaf_gont_symb( [], _Self, [], [], [] ).
gaf_gont_symb( [Row|Rows], Self, NonSymbs, MultSymbs, NewRows ) :-
arg( 5, Row, GoTermFull ),
% go_term( GoTermFull, GoTerm ),
go_obo_id( GoTermFull, GoTerm ),
arg( 11, Row, Bared ),
go_bared_symbol( Bared, Symb, Self, NonSymbs, MultSymbs, TNonSymbs, TMultSymbs ),
arg( 7, Row, Evid ),
( Symb == [] -> NewRows = TNewRows; NewRows= [row(GoTerm,Evid,Symb)|TNewRows] ),
gaf_gont_symb( Rows, Self, TNonSymbs, TMultSymbs, TNewRows ).
go_term( GoTermFull, GoTerm ) :-
(atom_concat('GO:',GoTermAtom,GoTermFull) ->
atom_number(GoTermAtom,GoTerm)
;
throw(no_go(GoTermFull))
).
go_bared_symbol( Bared, Symb, Self, NonSymbs, MultSymbs, TNonSymbs, TMultSymbs ) :-
atomic_list_concat( Parts, '|', Bared ),
map_succ_list( user:hgnc_symb, Parts, NestSymbs ),
flatten( NestSymbs, Symbs ),
go_bared_symbol_single( Symbs, Bared, Symb, Self, NonSymbs, MultSymbs, TNonSymbs, TMultSymbs ).
hgnc_symb( Symb, Symb ) :-
hgnc:hgnc_homs_symb_hgnc( Symb, _ ),
!.
hgnc_symb( Part, Symbs ) :-
atomic_list_concat( Subs, ':', Part ),
Subs \= [Part],
map_succ_list( hgnc_symb, Subs, Symbs ).
% This is a generic pattern...
go_bared_symbol_single( [], Bared, Symb, _Self, NonSymbs, MultSymbs, TNonSymbs, TMultSymbs ) :-
debuc( std_maps_gont(details), 'GO bared:~w did not lead to a symbol...', Bared ),
Symb = [],
NonSymbs = [Bared|TNonSymbs],
TMultSymbs = MultSymbs.
go_bared_symbol_single( [Symb], _Bared, Symb, _Self, NonSymbs, MultSymbs, TNonSymbs, TMultSymbs ) :-
!,
NonSymbs = TNonSymbs,
MultSymbs = TMultSymbs.
go_bared_symbol_single( [S1,S2|Sail], Bared, Symb, _Self, NonSymbs, MultSymbs, TNonSymbs, TMultSymbs ) :-
debuc( std_maps_gont(details), 'GO bared:~w did led to multiple symbols...,~w', [Bared,[S1,S2|Sail]] ),
memberchk( Symb, [S1,S2|Sail] ),
NonSymbs = TNonSymbs,
MultSymbs = [Bared-[S1,S2|Sail]|TMultSymbs].
clense_goa_hs( [H|T], Mtx ) :-
functor( H, _, 1 ),
!,
clense_goa_hs( T, Mtx ).
clense_goa_hs( Mtx, Mtx ).