Update examples

Author: RJMW

examples/run.py

@@ -1,64 +1,65 @@
 #!/usr/bin/python
 # -*- coding: utf-8 -*-
 
+import os
 from beams import in_out
+import networkx as nx
+from beams.grouping import group_features
 from beams.annotation import annotate_adducts
 from beams.annotation import annotate_isotopes
+from beams.annotation import annotate_oligomers
+from beams.annotation import annotate_multiple_charged_ions
 from beams.annotation import annotate_compounds
 from beams.annotation import annotate_molecular_formulae
 from beams.annotation import summary
+from beams import plots
+
 
 def main():
 
-    fn_peaklist = "../tests/test_data/variableMetadata.txt"
-    fn_matrix = "../tests/test_data/dataMatrix.txt"
+    path = "../tests/test_data/"
+    fn_peaklist = os.path.join(path, "variableMetadata.txt")
+    fn_matrix = os.path.join(path, "dataMatrix.txt")
 
-    #df = in_out.combine_peaklist_matrix(fn_peaklist, fn_matrix)
+    df = in_out.combine_peaklist_matrix(fn_peaklist, fn_matrix)
 
-    fn_matrix = "../tests/test_data/Study_pospeaks_both_parts_no_MPA.txt"
-    #df = in_out.read_xset_matrix(fn_matrix, first_sample="s1")
+    ion_mode = "pos"
 
-    fn_peaklist = "../tests/test_data/peaklist_dims_pos_theoretical.txt"
-    df = in_out.read_peaklist(fn_peaklist)
+    db_out = "results_{}.sqlite".format(ion_mode)
 
-    db_out = "../tests/test_data/results.sqlite"
+    graphs = group_features(df, db_out, max_rt_diff=5.0, coeff_thres=0.7, pvalue_thres=0.01, method="pearson")
 
-    #df = df[0:700]
-    #print(df)
-    #graph = group_features(df, db_out, max_rt_diff=5.0, coeff_thres=0.7, pvalue_thres=None, method="pearson")
+    nx.write_gml(graphs, "graphs.gml")
+    # graphs = nx.read_gml("graphs.gml")
 
-    #nx.write_gml(graph, "../tests/test_data/graph.gml")
-    #graph = nx.read_gml("../tests/test_data/graph.gml")
 
-    lib_isotopes = in_out.read_isotopes("../beams/data/isotopes.txt", "pos")
-    lib_adducts = in_out.read_adducts("../beams/data/adducts.txt", "pos")
-    lib_multiple_charged_ions = in_out.read_multiple_charged_ions("../beams/data/multiple_charged_ions.txt", "pos")
-    #lib_mass_differences = in_out.read_mass_differences("data/multiple_charged_differences.txt", "pos")
-    fn_mf = "../beams/data/trimMMD_sortAmass.txt"
-    fn_cpds = "../beams/data/trimMMD_sortMF.txt"
-    fn_sql_db = "../beams/data/MIDB_260916.sqlite"
+    path = "../beams/data"
+    lib_isotopes = in_out.read_isotopes(os.path.join(path, "isotopes.txt"), ion_mode)
+    lib_adducts = in_out.read_adducts(os.path.join(path, "adducts.txt"), ion_mode)
+    lib_multiple_charged_ions = in_out.read_multiple_charged_ions(os.path.join(path, "multiple_charged_ions.txt"), ion_mode)
+    lib_mass_differences = in_out.read_mass_differences(os.path.join(path, "multiple_charged_differences.txt"), ion_mode)
 
     print(lib_isotopes)
     print(lib_adducts)
-    print(lib_multiple_charged_ions)
 
     ppm = 5.0
 
-    #annotate_adducts(graph, db_out, ppm, lib_adducts)
-    annotate_adducts(df, db_out, ppm, lib_adducts)
-    #annotate_isotopes(graph, db_out, ppm, lib_isotopes)
-    #annotate_isotopes(df, db_out, ppm, lib_isotopes)
-    #annotate_oligomers(graphs, db_out, ppm, lib_adducts)
-    #annotate_artifacts(testdata_no_MPA, db_out, 0.005)
-    #annotate_multiple_charged_ions(graph, db_out, ppm, lib_multiple_charged_ions)
+    annotate_adducts(graphs, db_out, ppm, lib_adducts)
+    annotate_isotopes(graphs, db_out, ppm, lib_isotopes)
+    annotate_oligomers(graphs, db_out, ppm, lib_adducts)
+    annotate_multiple_charged_ions(graphs, db_out, ppm, lib_multiple_charged_ions)
 
-    annotate_molecular_formulae(df, lib_adducts, ppm, db_out, fn_mf)
-    #annotate_molecular_formulae(df, lib_adducts, ppm, db_out)
-    annotate_compounds(df, lib_adducts, ppm, db_out, fn_sql_db, "HMDB__25_09_2016")
+    # annotate_molecular_formulae(df, lib_adducts, ppm, db_out)
+    annotate_compounds(df, lib_adducts, ppm, db_out, "lipidmaps_full_20181217_v1")
 
     df_out = summary(df, db_out)
-    fn_out = "../tests/test_data/summary.txt"
-    df_out.to_csv(fn_out, sep="\t", index=False)
+    fn_out = "summary_{}.txt".format(ion_mode)
+    df_out.to_csv(fn_out, sep="\t", index=False, encoding="utf-8")
+
+    pdf_out = "report_{}.pdf".format(ion_mode)
+    plots.report(db=db_out, pdf_out=pdf_out, column_corr="r_value", column_pvalue="p_value",
+                 column_ppm_error="ppm_error", column_adducts="adduct")
+
 
 if __name__ == '__main__':
-    main()
+    main()