diff ipapy2_gibbs_sampler.py @ 0:7f84a8a5edde draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_gibbs_sampler.py	Fri May 16 08:00:41 2025 +0000
@@ -0,0 +1,133 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, GibbsArgumentParser, group_by_peak_id
+
+
+def main(
+    input_dataset_mapped_isotope_patterns,
+    input_dataset_annotations,
+    integrating_mode,
+    input_dataset_bio,
+    noits,
+    burn,
+    delta_bio,
+    delta_add,
+    all_out,
+    zs,
+    zs_out,
+    output_dataset,
+):
+    annotations_df = input_dataset_annotations
+    annotations_df["post"] = annotations_df["post"].replace("", 0)
+    annotations_df = annotations_df.replace("", None)
+    annotations = group_by_peak_id(annotations_df)
+
+    if not zs:
+        zs = None
+
+    if integrating_mode == "adducts":
+        zs = ipa.Gibbs_sampler_add(
+            input_dataset_mapped_isotope_patterns,
+            annotations,
+            noits=noits,
+            burn=burn,
+            delta_add=delta_add,
+            all_out=all_out,
+            zs=zs,
+        )
+    else:
+        if args.integrating_mode == "biochemical":
+            zs = ipa.Gibbs_sampler_bio(
+                input_dataset_mapped_isotope_patterns,
+                annotations,
+                Bio=input_dataset_bio,
+                noits=noits,
+                burn=burn,
+                delta_bio=delta_bio,
+                all_out=all_out,
+                zs=zs,
+            )
+        else:
+            zs = ipa.Gibbs_sampler_bio_add(
+                input_dataset_mapped_isotope_patterns,
+                annotations,
+                Bio=input_dataset_bio,
+                noits=noits,
+                burn=burn,
+                delta_bio=delta_bio,
+                delta_add=delta_add,
+                all_out=all_out,
+                zs=zs,
+            )
+
+    annotations_flat = flattern_annotations(annotations)
+    write_func, file_path = output_dataset
+    write_func(annotations_flat, file_path)
+
+    if args.all_out:
+        write_func, file_path = zs_out
+        write_func(zs, file_path)
+
+
+if __name__ == "__main__":
+    parser = GibbsArgumentParser(
+        description="""Gibbs sampler considering both biochemical and adducts connections. The
+    function computes the posterior probabilities of the annotations
+    considering the possible biochemical connections reported in Bio and the
+    possible adducts connection.""",
+    )
+    parser.add_argument(
+        "--input_dataset_mapped_isotope_patterns",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="a dataframe containing the measured intensities across several samples.",
+    )
+    parser.add_argument(
+        "--input_dataset_annotations",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="a datset containing the annotations of the features.",
+    )
+    parser.add_argument(
+        "--integrating_mode",
+        type=str,
+        required=True,
+        choices=["adducts", "biochemical", "biochemical_adducts"],
+        help=(
+            "The mode of integration. Options are 'adducts', 'biochemical', or"
+            " 'biochemical_adducts'."
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_bio",
+        nargs=2,
+        action="load_data",
+        type=str,
+        help="""dataframe (2 columns), reporting all the possible connections between
+         compounds. It uses the unique ids from the database. It could be the
+         output of Compute_Bio() or Compute_Bio_Parallel()""",
+    )
+    parser.add_argument(
+        "--delta_bio",
+        type=float,
+        help="""parameter used when computing the conditional priors. The
+               parameter must be positive. The smaller the parameter the more
+               weight the adducts connections have on the posterior
+               probabilities. Default 1.""",
+    )
+    args = parser.parse_args()
+    main(
+        args.input_dataset_mapped_isotope_patterns,
+        args.input_dataset_annotations,
+        args.integrating_mode,
+        args.input_dataset_bio,
+        args.noits,
+        args.burn,
+        args.delta_bio,
+        args.delta_add,
+        args.all_out,
+        args.zs,
+        args.zs_out,
+        args.output_dataset,
+    )