:- set_prolog_flag(stack_limit, 12 000 000 000).
% :- set_prolog_flag(stack_limit, 18 000 000 000). % try this
% if library(lib) is missing, install via pack_install(lib).
%
:- use_module(library(lib)).
:- lib(debug_call). % debuc/1,3
% external code, lib knowns how to deal with these (will install if missing)
:- lib(mtx).
% :- lib(bio_db).
:- lib(os_lib).
:- lib(by_unix).
:- lib(options).
:- lib(stoics_lib:url_file/3).
:- lib(stoics_lib:message_report/3).
:- lib(stoics_lib:portray_clauses/2).
% 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(unip:bio_db_build_downloads('unip/maps/map_unip_mouse_ensp_unip')).
% :- ensure_loaded(unip:bio_db_build_downloads('unip/maps/map_unip_mouse_mgim_unip')).
% :- ensure_loaded(mgim:bio_db_build_downloads('mgim/maps/map_mgim_mouse_mgim_unip')).
% :- ensure_loaded(mgim:bio_db_build_downloads('mgim/maps/map_mgim_mouse_mgim_symb')).
% local libs & sources
:- 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(portray_informed_clauses/4).
:- lib(url_file_local_date_mirror/3).
:- lib(std_graphs_strg_auto_version/1).
:- lib(bio_db_string_version_base_name/5). % uses bio_db_source_url/3
:- debuc(by_unix).
:- debuc(std_graphs_strg). % fixme:
std_mouse_graphs_strg_defaults( Args, Defs ) :-
Defs = [ db(strg),
debug(true),
debug_fetch(true),
debug_url(false),
iactive(true),
org(mouse),
relation(links)
| T
],
( std_graphs_strg_auto_version(Vers,Args) -> % let options/2 do the erroring
% because user might provide it
T = [string_version(Vers)]
;
T = []
).
% last good one: std_graphs_string( '10' ). 2016/09/08
% last good one: std_graphs_string( '10.5' ). 2018/03/30
/** std_mouse_graphs_strg( Opts ).
Mouse graphs for STRING protein protein interactions.
Depends on std_maps_mgim std_maps_unip.
Opts
* db(Db=strg)
source database
* debug(Dbg=true)
informational, progress messages
* debug_fetch(Fbg=false)
whether to debug the fetching of the url
* 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
* links_stem(Ltem='protein.links.v')
stem for the filename of the remote links file
* org(Org=mouse)
organism
* relation(Rel=links)
relation of STRING we are interested in (bio_db_string_version_base_name/5)
* string_version(Vers)
default is collected by visiting the STRING web-page
==
?- std_mouse_graphs_strg([]).
==
@author nicos angelopoulos
@version 0:2 2022/12/27,
@see https://string-db.org
@tbd this is closely related to the human pred, we should factor the common things out
*/
std_mouse_graphs_strg( Args ) :-
Self = std_mouse_graphs_strg,
options_append( Self, Args, Opts ),
bio_db_build_aliases( Opts ),
options( string_version(VersionPrv), Opts ),
% load necessary data that has already been generated
ensure_loaded(unip:bio_db_build_downloads('unip/maps/unip_musm_ensp_unip')),
ensure_loaded(unip:bio_db_build_downloads('unip/maps/unip_musm_mgim_unip')),
ensure_loaded(mgim:bio_db_build_downloads('mgim/maps/mgim_musm_mgim_unip')),
ensure_loaded(mgim:bio_db_build_downloads('mgim/maps/mgim_musm_mgim_symb')),
( number(VersionPrv) -> atom_number(Version,VersionPrv); Version = VersionPrv ),
% ensure_loaded( bio_db_build_aliases ),
debuc( Self, 'Version: ~w', Version ),
% std_graphs_string_version_base_name( Version, Bname, From ),
bio_db_string_version_base_name( Version, _VersD, RemBname, SrcUrl, Opts ),
debuc( Self, 'Remote base name: ~w', RemBname ),
% absolute_file_name( bio_db_build_downloads(strg), Parent ),
% os_path( Parent, VersD, DnlD ),
% os_make_path( DnlD, debug(true) ),
build_dnload_loc( Self, DnlD, Opts ),
debuc( Self, 'Downloading from: ~p', SrcUrl ),
url_file_local_date_mirror( SrcUrl, DnlD, [dnld_file(Bname),iface(wget)|Opts] ),
debuc( Self, 'Basename to work on: ~p', [Bname] ),
working_directory( Here, DnlD ),
@ gunzip( -k, -f, Bname ), % keeps .gz file
% @ gunzip( '9606.protein.links.v10.txt.gz' ),
% Edge = edge_strg_mouse,
EnspPn = strg_musm_edge_ensp,
file_name_extension( TxtF, gz, Bname ),
debuc( Self, 'Directory: ~p', [DnlD] ),
Mess1 = 'Converting string file: ~p, to Prolog',
debuc( Self, Mess1, [TxtF] ),
MtxOpts = [ csv_read(separator(0' )), predicate_name(EnspPn),
rows_transform(maplist(user:de_mouse)), header_remove(true)
],
mtx_prolog( TxtF, File, MtxOpts ),
debuc( Self, 'Wrote on file: ~p', [File] ),
delete_file( TxtF ),
% @ rm( -rf, graphs ), don't do that ! there are now multiple downloads from string..
os_make_path( graphs, debug(true) ),
% Trg = 'graphs/edge_strg_mouse.pl',
os_dir_stem_ext( graphs, EnspPn, pl, EnspRelF ),
@ rm( -f, EnspRelF ),
@ mv( File, EnspRelF ),
mouse_strg_symbolise_edges( Self, EnspPn, EnspRelF, UnoSymbEdges ),
sort( UnoSymbEdges, SymbEdges ),
length( SymbEdges, SymbEdgesLen ),
debuc( Self, 'unique symbol edges (mouse): ~w', [SymbEdgesLen] ),
EdgeSymbsF = 'graphs/strg_musm_edge_symb.pl',
bio_db_dnt_times( Bname, DnDt, _EndDt ),
EdgeSymbsInfos = [ source-SrcUrl, datetime-DnDt, header-header('Symbol','Symbol',weight),
data_types-data_types(atom,atom,integer)
],
portray_informed_clauses( SymbEdges, EdgeSymbsInfos, EdgeSymbsF, [] ),
% SymbOpts = [source(From),datetime(DnDt),header(row('MGI_Symbol','MGI_Symbol',weight))],
% bio_db_add_infos_to( SymbOpts, EdgeSymbsF ),
debuc( Self, wrote, EdgeSymbsF ),
MousOpts = [ source(SrcUrl), datetime(DnDt),
header(row('Ensembl_Protein','Ensembl_Protein',weight))
],
debuc( Self, task(stop), infosise(copy_stream(EnspRelF )) ),
bio_db_add_infos_to( MousOpts, EnspRelF ),
debuc( Self, task(stop), infosise(copy_stream) ),
link_to_bio_sub( strg, [EnspRelF,EdgeSymbsF], [org(mouse),type(graphs)] ),
working_directory( _, Here ).
% At 13:34:57 on 10th of Jun 2023 starting task: symbolise(streamed).
% At 13:37:29 on 10th of Jun 2023 stop task: symbolise(streamed).
%
mouse_strg_symbolise_edges( Self, EnspPn, EnspRelF, Edges ) :-
open( EnspRelF, read, InS ),
read( InS, Term ),
debuc( Self, task(start), symbolise(streamed) ),
mouse_strg_symbolise_edges_stream( Term, EnspPn, InS, Edges ),
debuc( Self, task(stop), symbolise(streamed) ),
close( InS ).
mouse_strg_symbolise_edges_stream( end_of_file, _Pn, _InS, Edges ) :-
!,
[] = Edges.
mouse_strg_symbolise_edges_stream( InTerm, Pn, InS, Edges ) :-
( functor(InTerm,Pn,3) ->
arg( 1, InTerm, EnsP1 ),
arg( 2, InTerm, EnsP2 ),
arg( 3, InTerm, W ),
( (ensp_mouse_symb( EnsP1, Symb1 ),
ensp_mouse_symb( EnsP2, Symb2 )) ->
sort_four( Symb1, Symb2, SymbA, SymbB ),
[strg_musm_edge_symb(SymbA,SymbB,W)|TEdges] = Edges
;
TEdges = Edges
)
;
throw(rogue_ensp_to_symb_term(InTerm))
),
read( InS, NxtTerm ),
mouse_strg_symbolise_edges_stream( NxtTerm, Pn, InS, TEdges ).
ensp_mouse_symb( EnsP, Symb ) :- % fixme: make sure the cut is green !
unip:unip_musm_ensp_unip( EnsP, Unip ),
( unip:unip_musm_mgim_unip(Mgim,Unip)
;
mgim:mgim_musm_mgim_unip(Mgim,Unip)
),
mgim:mgim_musm_mgim_symb( Mgim, Symb ),
!.
sort_four( X, Y, A, B ) :-
Y @< X,
!,
A = Y, B = X.
sort_four( A, B, A, B ).
de_mouse( row(MousEnsP1,MousEnsP2,WAtm), row(EnsP1,EnsP2,W) ) :-
atom_concat( '10090.', EnsP1, MousEnsP1 ),
atom_concat( '10090.', EnsP2, MousEnsP2 ),
( number(WAtm) -> W = WAtm; atom_number(WAtm,W) ),
!.
de_mouse( Row, _ ) :-
debuc( _, 'Failed to translate row: ~w', Row ),
abort.