diff benchmarking.py @ 1:867f17ede7f3 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp commit 42e5dfeaa309e6ac17b4616314498a3b628272d2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/benchmarking.py	Thu Sep 14 12:49:19 2023 +0000
@@ -0,0 +1,270 @@
+import argparse
+import os
+
+import numpy as np
+import pandas as pd
+
+# Define the ArgumentParser
+parser = argparse.ArgumentParser("List of natural abundances of the isotopes")
+
+parser.add_argument(
+    "--input", type=str, metavar="data", help="Input file/folder", required=True
+)
+
+parser.add_argument(
+    "--isotope_abundance_matrix",
+    type=str,
+    metavar="data",
+    help="Isotope abundance matrix",
+    required=True,
+)
+parser.add_argument(
+    "--isotope",
+    type=str,
+    metavar="ISOTOPE",
+    help="Isotope",
+    required=True,
+)
+parser.add_argument(
+    "--out_summary",
+    type=str,
+    metavar="output",
+    help="Peptide summary output",
+    required=False,
+)
+parser.add_argument(
+    "--out_filtered", type=str, metavar="output", help="Filtered output", required=False
+)
+parser.add_argument(
+    "--nominal_values",
+    type=str,
+    metavar="nominal_values",
+    help="Table giving nominal values",
+    default=None,
+    required=False,
+)
+
+# Indicate end of argument definitions and parse args
+args = parser.parse_args()
+
+
+def parse_nominal_values(filename):
+    nominal_values = {}
+    if not filename:
+        return nominal_values
+    with open(filename) as fh:
+        for line in fh:
+            line = line.strip()
+            if len(line) == 0 or line[0] == "#":
+                continue
+            line = line.split()
+            nominal_values[line[0]] = line[1]
+    return nominal_values
+
+
+# Benchmarking section
+# the functions for optimising calis-p data
+
+
+def load_calisp_data(filename, factor):
+    # (1) load data
+    file_count = 1
+    if os.path.isdir(filename):
+        file_data = []
+        file_count = len(os.listdir(filename))
+        for f in os.listdir(filename):
+            f = os.path.join(filename, f)
+            file_data.append(pd.read_feather(f))
+            base, _ = os.path.splitext(f)
+            file_data[-1].to_csv(f"{base}.tsv", sep="\t", index=False)
+        data = pd.concat(file_data)
+    else:
+        data = pd.read_feather(filename)
+        base, _ = os.path.splitext(filename)
+        data.to_csv(f"{base}.tsv", sep="\t", index=False)
+
+    file_success_count = len(data["ms_run"].unique())
+    # (2) calculate deltas
+    # ((1-f)/f) - 1 == 1/f -2
+    data["delta_na"] = data["ratio_na"] / ((1 / factor) - 2) * 1000
+    data["delta_fft"] = data["ratio_fft"] / ((1 / factor) - 2) * 1000
+    print(
+        f"Loaded {len(data.index)} isotopic patterns from {file_success_count}/{file_count} file(s)"
+    )
+    return data
+
+
+def filter_calisp_data(data, target):
+    if target.lower() == "na":
+        subdata = data.loc[
+            lambda df: (df["flag_peak_at_minus_one_pos"] == False)  # noqa: E712
+            & (df["flag_pattern_is_wobbly"] == False)  # noqa: E712
+            & (df["flag_psm_has_low_confidence"] == False)  # noqa: E712
+            & (df["flag_psm_is_ambiguous"] == False)  # noqa: E712
+            & (df["flag_pattern_is_contaminated"] == False)  # noqa: E712
+            & (df["flag_peptide_assigned_to_multiple_bins"] == False),  # noqa: E712
+            :,
+        ]
+    elif target.lower() == "fft":
+        subdata = data.loc[
+            lambda df: (df["error_fft"] < 0.001)
+            & (df["flag_peptide_assigned_to_multiple_bins"] == False),  # noqa: E712
+            :,
+        ]
+    elif target.lower() == "clumpy":
+        subdata = data.loc[
+            lambda df: (df["error_clumpy"] < 0.001)
+            & (df["flag_peptide_assigned_to_multiple_bins"] == False),  # noqa: E712
+            :,
+        ]
+
+    print(
+        f"{len(subdata.index)} ({len(subdata.index)/len(data.index)*100:.1f}%) remaining after filters."
+    )
+    return subdata
+
+
+def estimate_clumpiness(data):
+    subdata = data.loc[lambda df: df["error_clumpy"] < 0.001, :]
+    clumpiness = []
+    for c in ["c1", "c2", "c3", "c4", "c5", "c6"]:
+        try:
+            count, division = np.histogram(subdata[c], bins=50)
+            count = count[1:-1]
+            opt = 0.02 * np.where(count == count.max())[0][0] / 0.96
+            clumpiness.append(opt)
+        except ValueError:
+            pass
+    return clumpiness / sum(clumpiness)
+
+
+# the function for benchmarking
+def benchmark_sip_mock_community_data(data, factor, nominal_values):
+    background_isotope = 1 - factor
+    background_unlabelled = factor
+
+    # For false positive discovery rates we set the threshold at the isotope/unlabelled associated with 1/4 of a generation
+    # of labeling. The E. coli values (1.7, 4.2 and 7.1) are for 1 generation at 1, 5 and 10% label,
+    # and we take the background (1.07) into account as well.
+    thresholds = {
+        1: 1.07 + (1.7 - 1.07) / 4,
+        5: 1.07 + (4.2 - 1.07) / 4,
+        10: 1.07 + (7.1 - 1.07) / 4,
+    }
+
+    filenames = data["ms_run"].unique()
+    for fname in filenames:
+        print(f"Using nominal value {nominal_values.get(fname, 0)} for {fname}")
+
+    bin_names = data["bins"].unique()
+    peptide_sequences = data["peptide"].unique()
+    benchmarking = pd.DataFrame(
+        columns=[
+            "file",
+            "bins",
+            "% label",
+            "ratio",
+            "peptide",
+            "psm_mz",
+            "n(patterns)",
+            "mean intensity",
+            "ratio_NA median",
+            "N mean",
+            "ratio_NA SEM",
+            "ratio_FFT median",
+            "ratio_FFT SEM",
+            "False Positive",
+        ]
+    )
+    false_positives = 0
+    for p in peptide_sequences:
+        pep_data = data.loc[lambda df: df["peptide"] == p, :]
+        for b in bin_names:
+            # bindata = data.loc[lambda df: df["bins"] == b, :]
+            for f in filenames:
+                nominal_value = nominal_values.get(fname, 0)
+                unlabeled_fraction = 1 - nominal_value / 100
+                U = unlabeled_fraction * background_unlabelled
+                I = nominal_value / 100 + unlabeled_fraction * background_isotope
+                ratio = I / U * 100
+                pepfiledata = pep_data.loc[lambda df: df["ms_run"] == f, :]
+                is_false_positive = 0
+                try:
+                    if (
+                        b != "K12"
+                        and pepfiledata["ratio_na"].median() > thresholds[nominal_value]
+                    ):
+                        is_false_positive = 1
+                        false_positives += 1
+                except KeyError:
+                    pass
+                benchmarking.loc[len(benchmarking)] = [
+                    f,
+                    b,
+                    nominal_value,
+                    ratio,
+                    p,
+                    pepfiledata["psm_mz"].median(),
+                    len(pepfiledata.index),
+                    pepfiledata["pattern_total_intensity"].mean(),
+                    pepfiledata["ratio_na"].median(),
+                    pepfiledata["psm_neutrons"].mean(),
+                    pepfiledata["ratio_na"].sem(),
+                    pepfiledata["ratio_fft"].median(),
+                    pepfiledata["ratio_fft"].sem(),
+                    is_false_positive,
+                ]
+
+    benchmarking = benchmarking.sort_values(["bins", "peptide"])
+    benchmarking = benchmarking.reset_index(drop=True)
+    return benchmarking
+
+
+rowcol = {
+    "13C": (0, 1),
+    "14C": (0, 2),
+    "15N": (1, 1),
+    "17O": (2, 1),
+    "18O": (2, 2),
+    "2H": (3, 1),
+    "3H": (3, 2),
+    "33S": (4, 1),
+    "34S": (4, 2),
+    "36S": (4, 3),
+}
+with open(args.isotope_abundance_matrix) as iamf:
+    matrix = []
+    for line in iamf:
+        line = line.strip()
+        line = line.split("#")[0]
+        if line == "":
+            continue
+        matrix.append([float(x) for x in line.split()])
+factor = matrix[rowcol[args.isotope][0]][rowcol[args.isotope][1]]
+print(f"Using factor {factor}")
+
+
+# cleaning and filtering data
+data = load_calisp_data(args.input, factor)
+
+if args.out_filtered:
+    data = filter_calisp_data(data, "na")
+    data["peptide_clean"] = data["peptide"]
+    data["peptide_clean"] = data["peptide_clean"].replace("'Oxidation'", "", regex=True)
+    data["peptide_clean"] = data["peptide_clean"].replace(
+        "'Carbamidomethyl'", "", regex=True
+    )
+    data["peptide_clean"] = data["peptide_clean"].replace(r"\s*\[.*\]", "", regex=True)
+
+    data["ratio_na"] = data["ratio_na"] * 100
+    data["ratio_fft"] = data["ratio_fft"] * 100
+    data.to_csv(args.out_filtered, sep="\t", index=False)
+
+    # The column "% label" indicates the amount of label applied (percentage of label in the glucose). The amount of
+    # labeled E. coli cells added corresponded to 1 generation of labeling (50% of E. coli cells were labeled in
+    # all experiments except controls)
+
+if args.out_summary:
+    nominal_values = parse_nominal_values(args.nominal_values)
+    benchmarks = benchmark_sip_mock_community_data(data, factor, nominal_values)
+    benchmarks.to_csv(args.out_summary, sep="\t", index=False)