:- set_prolog_flag(allow_dot_in_atom,false).
:- set_prolog_flag(stack_limit, 8 000 000 000).
:- use_module(library(csv)). % csv_read_file/2.
:- use_module(library(lists)). % member/2.
:- use_module(library(apply)). % maplist/4.
% :- use_module(library(debug)). % /1,3. -> debug_call
:- 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(os_lib).
:- lib(options).
:- lib(debug_call). % debuc/1,3.
:- lib(stoics_lib:map_list_options/3).
% also sets lib alias to that dir
:- ensure_loaded('../../lib/bio_db_build_aliases'). % /1.
% local libs & sources
:- lib(map_uniprot/4).
:- lib(csv_ids_map/6).
:- lib(link_to_bio_sub/3).
:- lib(build_dnload_loc/3).
:- lib(bio_db_dnt_times/3).
:- lib(bio_db_add_infos/1). % bio_db_add_infos_to/2.
:- lib(bio_db_source_url/3).
:- lib(url_file_local_date_mirror/3).
% 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' ).
std_mouse_maps_unip_defaults( Defs ) :-
Defs = [ db(unip),
debug(true),
debug_fetch(true),
debug_url(false),
org(mouse),
unip_file_full('MOUSE_10090_idmapping.dat.gz'),
unip_file_sele('MOUSE_10090_idmapping_selected.tab.gz')
].
/** std_mouse_maps_unip(+Opts).
Create some 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)
* org(Org=mouse)
organism
* unip_file_full(Uff='MOUSE_10090_idmapping.dat.gz'
remote file name for Unip protein downloads (all proteins)
* unip_file_sele(Ufs='MOUSE_10090_idmapping_selected.tab.gz')
remote file name for Unip downloads (selected, annotated proteins- subset of Uff)
==
?- maps_std_uniprot.
?- shell( 'wc -l uniprot_*' ).
οÏÎÏÏηÏ;build_repo/mouse% date ; pupsh std_mouse_maps_unip.pl ; date
Tue 27 Dec 16:05:52 GMT 2022
% Building at: '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27'
% Loc: '/home/nicos/.local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27/dnloads/unip'
...
Tue 27 Dec 16:06:57 GMT 2022
οÏÎÏÏηÏ;unip/maps% date
Tue 27 Dec 16:08:45 GMT 2022
οÏÎÏÏηÏ;unip/maps% pwd
/usr/local/users/nicos/local/share/swi-prolog/pack/Downloads/bio_db_repo-22.12.27/dnloads/unip/maps
οÏÎÏÏηÏ;unip/maps% wc -l *_m*
67172 unip_musm_ensp_unip.pl
28758 unip_musm_gyno_unip.pl
80455 unip_musm_mgim_unip.pl
129676 unip_musm_trem_nucs.pl
32782 unip_musm_unip_ncbi.pl
83182 unip_musm_unip_symb.pl
422025 total
==
@author nicos angelopoulos
@version 0.2 2015/4/27
@version 0.3 2023/9/25 use more local libs and control via options
*/
std_mouse_maps_unip( Args ) :-
Self = std_mouse_maps_unip,
options_append( Self, Args, Opts ),
bio_db_build_aliases( Opts ),
build_dnload_loc( Self, DnDir, Opts ),
/* double check unip part works with the nucl part // 15.05.15 */
working_directory( Old, DnDir ),
% unip_mouse( Url ),
bio_db_source_url( Url, [debug_url-debug,unip_file_full-url_file], Opts ),
% url_file( Url,
UrlOpts = [debug(true),interface(wget),dnld_file(File)],
options( debug_fetch(Fbg), Opts ),
url_file_local_date_mirror( Url, DnDir, [debug(Fbg)|UrlOpts] ),
os_make_path( maps, debug(true) ),
debuc( Self, 'Dir location: ~p', DnDir ),
Rev = [id_map('MOUSE_10090_idmapping.dat'),org(mouse),f_call(de_vers),interface(prolog),reverse(true)],
map_uniprot( 'Ensembl_PRO', Csv, [EnspF], Rev ),
Sem = [interface(prolog),f_call(de_semi('MGI')),reverse(true),id_map('MOUSE_10090_idmapping.dat'),org(mouse)],
map_uniprot( 'MGI', Csv, [MgiF], Sem ),
Ifc = [id_map('MOUSE_10090_idmapping.dat'),org(mouse),interface(prolog)],
Rfc = [id_map('MOUSE_10090_idmapping.dat'),org(mouse),interface(prolog),reverse(true)],
map_uniprot( 'GeneID', Csv, [EtzF], Ifc ),
% map_uniprot( 'UniGene', Csv, [UniGF], Ifc ),
map_uniprot( 'Gene_Name', Csv, [SymbF], Ifc ),
map_uniprot( 'Gene_Synonym', Csv, [GynoF], Rfc ),
% Files = [HgncF,FromHgncF,EtzF,UniGF,EnspF],
% Files = [MgiF,EtzF,UniGF,EnspF,SymbF,GynoF],
Files = [MgiF,EtzF,EnspF,SymbF,GynoF],
link_to_bio_sub( unip, Files, [org(mouse),type(maps)] ),
bio_db_dnt_times( File, SwDnDt, _SwDnEn ),
SwOpts = [source(Url),datetime(SwDnDt)],
bio_db_add_infos_to( [header(row('Ensembl_Protein','UniProt'))|SwOpts], 'maps/unip_musm_ensp_unip.pl' ),
bio_db_add_infos_to( [header(row('Uni_Protein','Entrez_ID'))|SwOpts], 'maps/unip_musm_unip_ncbi.pl' ),
bio_db_add_infos_to( [header(row('Uni_Protein','MGI'))|SwOpts], 'maps/unip_musm_mgim_unip.pl' ),
% bio_db_add_infos_to( [header(row('Uni Protein','HGNC ID'))|SwOpts], 'maps/map_unip_mouse_unip_hgnc.pl' ),
% Unigene has been discontinued
%bio_db_add_infos_to( [header(row('Uni_Protein','Uni_Gene'))|SwOpts], 'maps/map_unip_mouse_unip_unig.pl' ),
bio_db_add_infos_to( [header(row('Uni_Protein','Symbol'))|SwOpts], 'maps/unip_musm_unip_symb.pl' ),
bio_db_add_infos_to( [header(row('Symbol','Uni_Protein'))|SwOpts], 'maps/unip_musm_gyno_unip.pl' ),
working_directory( _, DnDir ),
bio_db_source_url( TremUrl, [debug_url-debug,unip_file_sele-url_file], Opts ),
% 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),dnld_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 ),
% @ pwd(),
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_rows/TremRows ),
% 17/22
findall( unip_musm_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_len/TNRows ),
sort( TNRows, TNOrdRows ),
open( '../maps/unip_musm_trem_nucs.pl', write, TNOut ),
maplist( portray_clause(TNOut), TNOrdRows ),
close( TNOut ),
working_directory( _, '../maps' ),
link_to_bio_sub( unip, 'unip_musm_trem_nucs.pl', [org(mouse),type(maps)] ),
TrOpts = [source(TremUrl),datetime(TrDnDt),header(row('treMBLE_Protein','Nucleotide_Sequence'))],
bio_db_add_infos_to( TrOpts, 'unip_musm_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 ),
debug_call( 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_map_sub( unip, AbsMapF ).
link_to_bio_sub( unip, AbsMapF, [org(mouse),type(maps)] ).
*/
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 ).
os_rm_rf( Dir ) :-
exists_directory(Dir) ->
delete_directory_and_contents(Dir),
!.
os_rm_rf( _Dir ).
de_vers( Prv, Cln ) :-
atomic_list_concat( [Cln,Ver], '.', Prv ),
atom_number( Ver, _ ),
!.
de_vers( Cln, Cln ).
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.