Add test data

setup.py

+from setuptools import setup, find_packages
+
+setup(name="metabolites_mapping",
+      version='0.0.1',
+      author='Mathieu UMEC',
+      author_email='mathieu.umec@inrae.fr',
+      description="A package for process mapping and contextualisation",
+      package=find_packages(),
+      install_requires=["bs4 >= 0.0.1", "docx >= 0.2.4", "fpdf2 >= 2.7.8",
+                        "mysql-connector-python >= 8.4.0", "numpy >= 1.24.3",
+                        "pandas >= 1.5.3", "py4cytoscape >= 1.9.0",
+                        "requests >= 2.31.0", "seaborn >= 0.12.2",
+                        "scipy >= 1.11.1", "scikit-learn >= 1.3.0",
+                        "urllib3 >= 2.0.3", "xmltodict >= 0.13.0"],
+      python_requires=">=3.10",
+      classifiers=["Development Status :: 3 - Alpha",
+                   "License :: Other/Proprietary License",
+                   "Operating System :: OS Independent"]
+    )

src/processing_mapping_results/Tests_unitaires/Cors_file_for_test/Corres_file_for_CPDB_unittest.csv

-inosine;17596
-L-glutamic acid;16015
-pyruvic acid;32816

src/processing_mapping_results/Tests_unitaires/Cors_file_for_test/Corres_file_for_RAMP_unittest.csv

-inosine;chebi:17596
-L-glutamic acid;chebi:16015
-pyruvic acid;chebi:32816

src/processing_mapping_results/Tests_unitaires/test_data/conversion_metabolites_id/id_conv_opti/MA_data_test.csv

+Query;Match;HMDB;PubChem;ChEBI;KEGG;METLIN;SMILES;Comment
+25858;Paraxanthine;HMDB0001860;4687;25858;C13747;1457;CN1C=NC2=C1C(=O)N(C)C(=O)N2;1
+18183;Pyroglutamic acid;HMDB0000267;7405;18183;C01879;3251;OC(=O)[C@@H]1CCC(=O)N1;1
+17712;Xanthine;HMDB0000292;1188;17712;C00385;82;O=C1NC2=C(NC=N2)C(=O)N1;1
+16359;Cholic acid;HMDB0000619;221493;16359;C00695;206;C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C;1
+30769;Citric acid;HMDB0000094;311;30769;C00158;124;OC(=O)CC(O)(CC(O)=O)C(O)=O;1
+28834;Deoxycholic acid;HMDB0000626;222528;28834;C04483;265;[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC[C@]4([H])C[C@H](O)CC[C@]4(C)[C@@]3([H])C[C@H](O)[C@]12C)[C@H](C)CCC(O)=O;1

src/processing_mapping_results/Tests_unitaires/test_data/conversion_metabolites_id/id_conv_opti/RaMP_data_test.csv

+chem_data_source;chem_source_id;iso_smiles;inchi_key_prefix;inchi_key;inchi;mw;monoisotop_mass;common_name;mol_formula
+chebi;chebi:30769;OC(=O)CC(O)(CC(O)=O)C(O)=O;KRKNYBCHXYNGOX;KRKNYBCHXYNGOX-UHFFFAOYSA-N;InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12);;192.027;citric acid;C6H8O7
+chebi;chebi:18183;OC(=O)[C@@H]1CCC(=O)N1;ODHCTXKNWHHXJC;ODHCTXKNWHHXJC-VKHMYHEASA-N;InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/t3-/m0/s1;;129.043;5-oxo-L-proline;C5H7NO3
+chebi;chebi:17712;O=c1[nH]c2[nH]cnc2c(=O)[nH]1;LRFVTYWOQMYALW;LRFVTYWOQMYALW-UHFFFAOYSA-N;InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11);;152.033;9H-xanthine;C5H4N4O2
+chebi;chebi:16359;[H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])C[C@H](O)[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC(O)=O;BHQCQFFYRZLCQQ;BHQCQFFYRZLCQQ-OELDTZBJSA-N;InChI=1S/C24H40O5/c1-13(4-7-21(28)29)16-5-6-17-22-18(12-20(27)24(16,17)3)23(2)9-8-15(25)10-14(23)11-19(22)26/h13-20,22,25-27H,4-12H2,1-3H3,(H,28,29)/t13-,14+,15-,16-,17+,18+,19-,20+,22+,23+,24-/m1/s1;;408.288;cholic acid;C24H40O5
+chebi;chebi:28834;[H][C@]12CC[C@@]3([H])[C@]4([H])CC[C@]([H])([C@H](C)CCC(O)=O)[C@@]4(C)[C@@H](O)C[C@]3([H])[C@@]1(C)CC[C@@H](O)C2;KXGVEGMKQFWNSR;KXGVEGMKQFWNSR-LLQZFEROSA-N;InChI=1S/C24H40O4/c1-14(4-9-22(27)28)18-7-8-19-17-6-5-15-12-16(25)10-11-23(15,2)20(17)13-21(26)24(18,19)3/h14-21,25-26H,4-13H2,1-3H3,(H,27,28)/t14-,15-,16-,17+,18-,19+,20+,21+,23+,24-/m1/s1;;392.293;deoxycholic acid;C24H40O4
+chebi;chebi:25858;Cn1cnc2[nH]c(=O)n(C)c(=O)c12;QUNWUDVFRNGTCO;QUNWUDVFRNGTCO-UHFFFAOYSA-N;InChI=1S/C7H8N4O2/c1-10-3-8-5-4(10)6(12)11(2)7(13)9-5/h3H,1-2H3,(H,9,13);;180.065;1,7-dimethylxanthine;C7H8N4O2

src/processing_mapping_results/Tests_unitaires/test_data/conversion_metabolites_id/id_conv_opti/cts_data_test.csv

+ChEBI;ChEBI;Chemical Name;Human Metabolome Database;InChIKey;Score;KEGG
+CHEBI:25858;CHEBI:25858;1,7-dimethyl-3H-purine-2,6-dione;HMDB0001860;QUNWUDVFRNGTCO-UHFFFAOYSA-N;1;C13747
+CHEBI:18183;CHEBI:18183;(2S)-5-oxo-2-pyrrolidinecarboxylic acid;HMDB0000267;ODHCTXKNWHHXJC-VKHMYHEASA-N;1;C01879
+CHEBI:17712;CHEBI:17712;3,7-dihydropurine-2,6-dione;HMDB0000292;LRFVTYWOQMYALW-UHFFFAOYSA-N;1;C00385
+CHEBI:16359;CHEBI:16359;E1000;HMDB0000619;BHQCQFFYRZLCQQ-OELDTZBJSA-N;1;C00695
+CHEBI:30769;CHEBI:30769;2-hydroxypropane-1,2,3-tricarboxylic acid;HMDB0000094;KRKNYBCHXYNGOX-UHFFFAOYSA-N;1;C00158
+CHEBI:28834;CHEBI:28834;5b-Deoxycholate;HMDB0000626;KXGVEGMKQFWNSR-LLQZFEROSA-N;1;C04483

src/processing_mapping_results/Tests_unitaires/test_data/conversion_metabolites_id/id_conv_opti/metanetx_data_test.csv

+#query;mnx_id;reference;xrefs;InChIkey;InChI;SMILES;name
+chebi:25858;MNXM758;chebi:25858;CHEBI:25858 ... chebi:25858 ... chebi:34067 ... deprecated:MNXM90489 ... envipath:32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ee9af8fa-7c53-4a99-9f60-df9c3fd407b0 ... envipath:650babc9-9d68-4b73-9332-11972ca26f7b/compound/36b5dc09-a445-4b4c-810d-a80498a80e4f ... envipathM:32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ee9af8fa-7c53-4a99-9f60-df9c3fd407b0 ... envipathM:650babc9-9d68-4b73-9332-11972ca26f7b/compound/36b5dc09-a445-4b4c-810d-a80498a80e4f ... hmdb:HMDB0001860 ... hmdb:HMDB01860 ... kegg.compound:C13747 ... keggC:C13747 ... keggC:M_C13747 ... metacyc.compound:1-7-DIMETHYLXANTHINE ... metacycM:1-7-DIMETHYLXANTHINE ... reactome:R-ALL-158687 ... reactome:R-ALL-76424 ... reactomeM:R-ALL-158687 ... reactomeM:R-ALL-76424 ... sabiork.compound:20386 ... sabiorkM:20386 ... seed.compound:cpd09576 ... seedM:M_cpd09576 ... seedM:cpd09576;QUNWUDVFRNGTCO-UHFFFAOYSA-N;InChI=1S/C7H8N4O2/c1-10-3-8-5-4(10)6(12)11(2)7(13)9-5/h3H,1-2H3,(H,9,13);Cn1c(=O)[nH]c2ncn(C)c2c1=O;1,7-dimethylxanthine
+chebi:18183;MNXM722719;chebi:58402;CHEBI:16010 ... CHEBI:18183 ... CHEBI:57606 ... CHEBI:58402 ... bigg.metabolite:5oxpro ... biggM:5oxpro ... biggM:M_5oxpro ... chebi:12153 ... chebi:12157 ... chebi:16010 ... chebi:18183 ... chebi:20619 ... chebi:20624 ... chebi:2113 ... chebi:2116 ... chebi:44704 ... chebi:44943 ... chebi:57606 ... chebi:58402 ... deprecated:MNXM38283 ... deprecated:MNXM680977 ... deprecated:MNXM680991 ... deprecated:MNXM90283 ... deprecated:MNXM964 ... hmdb:HMDB0000267 ... hmdb:HMDB0000805 ... hmdb:HMDB00267 ... hmdb:HMDB0060262 ... hmdb:HMDB00805 ... hmdb:HMDB60262 ... kegg.compound:C01879 ... keggC:C01879 ... keggC:M_C01879 ... metacyc.compound:5-OXOPROLINE ... metacycM:5-OXOPROLINE ... reactome:R-ALL-1247942 ... reactomeM:R-ALL-1247942 ... sabiork.compound:2329 ... sabiork.compound:2392 ... sabiorkM:2329 ... sabiorkM:2392 ... seed.compound:cpd01293 ... seedM:M_cpd01293 ... seedM:cpd01293;ODHCTXKNWHHXJC-VKHMYHEASA-M;InChI=1S/C5H7NO3/c7-4-2-1-3(6-4)5(8)9/h3H,1-2H2,(H,6,7)(H,8,9)/p-1/t3-/m0/s1;O=C1CC[C@@H](C(=O)[O-])N1;5-oxo-L-proline
+chebi:17712;MNXM174;chebi:17712;CHEBI:15318 ... CHEBI:17712 ... CHEBI:48517 ... bigg.metabolite:xan ... biggM:M_xan ... biggM:xan ... chebi:10059 ... chebi:15318 ... chebi:17712 ... chebi:27317 ... chebi:46377 ... chebi:48517 ... deprecated:MNXM113964 ... deprecated:MNXM89783 ... envipath:32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75 ... envipath:650babc9-9d68-4b73-9332-11972ca26f7b/compound/b14521b6-e87b-4a2b-9964-2987bb80fd40 ... envipathM:32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75 ... envipathM:650babc9-9d68-4b73-9332-11972ca26f7b/compound/b14521b6-e87b-4a2b-9964-2987bb80fd40 ... hmdb:HMDB0000292 ... hmdb:HMDB00292 ... kegg.compound:C00385 ... keggC:C00385 ... keggC:M_C00385 ... metacyc.compound:XANTHINE ... metacycM:XANTHINE ... reactome:R-ALL-30064 ... reactomeM:R-ALL-30064 ... sabiork.compound:1871 ... sabiorkM:1871 ... seed.compound:cpd00309 ... seedM:M_cpd00309 ... seedM:cpd00309;LRFVTYWOQMYALW-UHFFFAOYSA-N;InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11);O=c1[nH]c(=O)c2nc[nH]c2[nH]1;xanthine
+chebi:16359;MNXM735592;chebi:29747;CHEBI:16359 ... CHEBI:29747 ... SLM:000000859 ... bigg.metabolite:cholate ... biggM:M_cholate ... biggM:cholate ... chebi:11895 ... chebi:13978 ... chebi:16359 ... chebi:1694 ... chebi:20216 ... chebi:20223 ... chebi:23168 ... chebi:23210 ... chebi:29747 ... chebi:41494 ... chebi:57748 ... deprecated:MNXM40830 ... deprecated:MNXM450 ... deprecated:MNXM735593 ... hmdb:HMDB0000505 ... hmdb:HMDB0000619 ... hmdb:HMDB00505 ... hmdb:HMDB00619 ... kegg.compound:C00695 ... kegg.drug:D10699 ... keggC:C00695 ... keggC:M_C00695 ... keggD:D10699 ... keggD:M_D10699 ... lipidmaps:LMST04010001 ... lipidmapsM:LMST04010001 ... metacyc.compound:CHOLATE ... metacycM:CHOLATE ... reactome:R-ALL-192431 ... reactome:R-ALL-193451 ... reactome:R-ALL-193473 ... reactome:R-ALL-444831 ... reactomeM:R-ALL-192431 ... reactomeM:R-ALL-193451 ... reactomeM:R-ALL-193473 ... reactomeM:R-ALL-444831 ... sabiork.compound:5188 ... sabiorkM:5188 ... seed.compound:cpd00526 ... seedM:M_cpd00526 ... seedM:cpd00526 ... slm:000000859;BHQCQFFYRZLCQQ-OELDTZBJSA-M;InChI=1S/C24H40O5/c1-13(4-7-21(28)29)16-5-6-17-22-18(12-20(27)24(16,17)3)23(2)9-8-15(25)10-14(23)11-19(22)26/h13-20,22,25-27H,4-12H2,1-3H3,(H,28,29)/p-1/t13-,14+,15-,16-,17+,18+,19-,20+,22+,23+,24-/m1/s1;C[C@H](CCC(=O)[O-])[C@H]1CC[C@H]2[C@H]3[C@H](C[C@H](O)[C@@]21C)[C@@]1(C)CC[C@@H](O)C[C@H]1C[C@H]3O;cholate
+chebi:30769;MNXM1107753;chebi:16947;CHEBI:133748 ... CHEBI:16947 ... CHEBI:30769 ... CHEBI:35802 ... CHEBI:35804 ... CHEBI:35806 ... CHEBI:35808 ... CHEBI:35809 ... CHEBI:35810 ... CHEBI:76049 ... bigg.metabolite:cit ... biggM:M_cit ... biggM:cit ... chebi:133748 ... chebi:13999 ... chebi:16947 ... chebi:23321 ... chebi:23322 ... chebi:30769 ... chebi:35802 ... chebi:35804 ... chebi:35806 ... chebi:35808 ... chebi:35809 ... chebi:35810 ... chebi:3727 ... chebi:41523 ... chebi:42563 ... chebi:76049 ... deprecated:MNXM727996 ... deprecated:MNXM727998 ... deprecated:MNXM727999 ... deprecated:MNXM728000 ... envipath:650babc9-9d68-4b73-9332-11972ca26f7b/compound/cb525a90-920b-49d9-b0fc-c42655323a65 ... envipathM:650babc9-9d68-4b73-9332-11972ca26f7b/compound/cb525a90-920b-49d9-b0fc-c42655323a65 ... hmdb:HMDB0000094 ... hmdb:HMDB00094 ... kegg.compound:C00158 ... kegg.drug:D00037 ... keggC:C00158 ... keggC:M_C00158 ... keggD:D00037 ... keggD:M_D00037 ... metacyc.compound:CIT ... metacycM:CIT ... reactome:R-ALL-29654 ... reactome:R-ALL-433138 ... reactome:R-ALL-76190 ... reactomeM:R-ALL-29654 ... reactomeM:R-ALL-433138 ... reactomeM:R-ALL-76190 ... sabiork.compound:1952 ... sabiorkM:1952 ... seed.compound:cpd00137 ... seedM:M_cpd00137 ... seedM:cpd00137;KRKNYBCHXYNGOX-UHFFFAOYSA-K;InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)/p-3;O=C([O-])CC(O)(CC(=O)[O-])C(=O)[O-];citrate
+chebi:28834;MNXM738432;chebi:23614;CHEBI:23614 ... CHEBI:28834 ... SLM:000485699 ... bigg.metabolite:dchac ... biggM:M_dchac ... biggM:dchac ... chebi:1687 ... chebi:23614 ... chebi:23616 ... chebi:28834 ... chebi:42317 ... deprecated:MNXM57907 ... deprecated:MNXM738433 ... hmdb:HMDB0000626 ... hmdb:HMDB00626 ... kegg.compound:C04483 ... kegg.drug:D10781 ... keggC:C04483 ... keggC:M_C04483 ... keggD:D10781 ... keggD:M_D10781 ... lipidmaps:LMST04010040 ... lipidmapsM:LMST04010040 ... metacyc.compound:DEOXYCHOLATE ... metacycM:DEOXYCHOLATE ... reactome:R-ALL-444851 ... reactome:R-ALL-5340204 ... reactomeM:R-ALL-444851 ... reactomeM:R-ALL-5340204 ... sabiork.compound:7345 ... sabiorkM:7345 ... seed.compound:cpd02733 ... seedM:M_cpd02733 ... seedM:cpd02733 ... slm:000485699;KXGVEGMKQFWNSR-LLQZFEROSA-M;InChI=1S/C24H40O4/c1-14(4-9-22(27)28)18-7-8-19-17-6-5-15-12-16(25)10-11-23(15,2)20(17)13-21(26)24(18,19)3/h14-21,25-26H,4-13H2,1-3H3,(H,27,28)/p-1/t14-,15-,16-,17+,18-,19+,20+,21+,23+,24-/m1/s1;C[C@H](CCC(=O)[O-])[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@@]21C;deoxycholate

src/processing_mapping_results/Tests_unitaires/test_data/network_visualization/data_intens_test.csv

+Chebi;intensité_cas;intensité_témoin
+15354;2528399.24;3627347.76
+16919;724776.17;521925.59
+15729;552441.75;710182.08
+17368;391830.73;508308.36
+16015;89797.84;123591.04
+15971;17534.42;140754.56
+17295;1383333.80;1545052.89
+16946;3967.13;4953.49

src/processing_mapping_results/Tests_unitaires/test_data/network_visualization/ora_cpdb_tests.csv

+p-value;q-value;pathway;source;external_id;members_input_overlap;members_input_overlap_geneids;size;effective_size
+1.52540814501e-06;5.07198208214e-05;Amino acid transport across the plasma membrane;Reactome;R-HSA-352230;17295, 15729, 16015, 15971;k:C00025, k:C00077, k:C00135, k:C00079;32;32
+1.96058984417e-06;5.2151689855e-05;Tryptophan catabolism;Reactome;R-HSA-71240;17295, 16015, 15971, 16946;k:C00025, k:C00135, k:C00079, k:C00328;34;34
+3.5086329322e-06;7.77746966638e-05;SLC-mediated transmembrane transport;Reactome;R-HSA-425407;15729, 15354, 16015, 15971, 17295, 17368;k:C00114, k:C00077, k:C00079, k:C00025, k:C00262, k:C00135;164;164
+6.13371244649e-06;0.000116540536483;Metabolism of amino acids and derivatives;Reactome;R-HSA-71291;16919, 15729, 16946, 15354, 16015, 15971, 17295;k:C00300, k:C00079, k:C00114, k:C00025, k:C00328, k:C00135, k:C00077;286;286
+1.39135058222e-05;0.000231312034295;Transport of inorganic cations/anions and amino acids/oligopeptides;Reactome;R-HSA-425393;17295, 15729, 16015, 15971;k:C00025, k:C00077, k:C00135, k:C00079;55;55
+1.87316008384e-05;0.000276811434612;Transport of small molecules;Reactome;R-HSA-382551;15729, 15354, 16015, 15971, 17295, 17368;k:C00114, k:C00077, k:C00025, k:C00262, k:C00135, k:C00079;219;219

src/processing_mapping_results/Tests_unitaires/test_data/ontology_gap/data_test_ontology_gap_kegg_chebi.csv

+Kegg;ID chebi
+C00157;chebi:16110
+C03631;NA
+NA;chebi:17636
+C00422  ;chebi:17855