seer-pas-sdk 1.1.1__py3-none-any.whl → 1.2.1__py3-none-any.whl

seer_pas_sdk/core/unsupported.py

@@ -4,6 +4,7 @@ seer_pas_sdk.core.unsupported -- in development
 
 import os
 import shutil
+from pathlib import Path
 
 from typing import List as _List
 
@@ -827,20 +828,29 @@ class _UnsupportedSDK(_SeerSDK):
             )
 
         # Step 1: Check if paths and file extensions are valid.
+        invalid_d_zip_files = []
         for file in ms_data_files:
             if not valid_ms_data_file(file):
                 raise ValueError(
                     "Invalid file or file format. Please check your file."
                 )
+            if file.endswith(".d.zip") and (not validate_d_zip_file(file)):
+                invalid_d_zip_files.append(file)
+
+        if invalid_d_zip_files:
+            raise ValueError(
+                f"The following .d.zip files are invalid: {', '.join(invalid_d_zip_files)}. Please check your files."
+            )
 
         extensions = set(
-            [os.path.splitext(file.lower())[1] for file in ms_data_files]
+            ["".join(Path(file).suffixes) for file in ms_data_files]
         )
 
         if filenames and ".d.zip" in extensions:
             raise ValueError(
                 "Please leave the 'filenames' parameter empty when working with .d.zip files. SeerSDK.rename_d_zip_file() is available for this use case."
             )
+
         # Step 2: Use active tenant to fetch the tenant_id.
         tenant_id = self.get_active_tenant_id()
 
@@ -1461,36 +1471,70 @@ class _UnsupportedSDK(_SeerSDK):
         Get analyte intensities data for a given PAS analysis.
         Args:
             analysis_id (str): ID of the analysis.
-            analyte_type (str): Type of the analyte. Must be either 'protein', 'peptide', precursor.
+            analyte_type (str): Type of the analyte. Must be either 'protein', 'peptide', 'precursor'.
             rollup (str): Intensities rollup method. Must be either 'np' or 'panel'.
-            norm_method (str): Search engine. Supported engines are: raw, engine, median, median80, pepcal. Default is 'pepcal'.
+            norm_method (str): Search engine. Supported engines are: raw, engine, median, median80, pepcal, pepcal_batch. Default is 'pepcal'.
 
         Returns:
             pd.DataFrame: A dataframe with each row containing the analyte intensity measurement:
                             'msrun_id', 'sample_id', 'nanoparticle' (if rollup is 'np'), 'protein_group', 'peptide' (for 'peptide' and 'precursor' analyte types), 'charge' (for 'precursor' analyte type),
                             'intensity_log10', 'protein_group_q_value', 'q_value' (for 'precursor' analyte type), 'rt' and 'irt' (for 'peptide' and 'precursor' analyte types)
         """
-        # 1. Get msrun data for analysis
+
+        def filepath_to_msrunid(filepath):
+            return os.path.basename(filepath).split(".")[0]
+
+        # 1. Get samples and msrun data for analysis
         samples = self.find_samples(analysis_id=analysis_id)
-        sample_name_to_id = {s["sample_name"]: s["id"] for s in samples}
-        # for np rollup, a row represents an msrun
-        msruns = self.find_msruns(sample_ids=sample_name_to_id.values())
-        file_to_msrun = {
-            os.path.basename(msrun["raw_file_path"]).split(".")[0]: msrun
-            for msrun in msruns
-        }
-        sample_to_msrun = {msrun["sample_id"]: msrun for msrun in msruns}
 
-        # for panel rollup, a row represents a sample
+        sample_uuid_to_id = {s["id"]: s["sample_id"] for s in samples}
+        sample_id_to_uuid = {s["sample_id"]: s["id"] for s in samples}
+        # FIXME sample_name is not guaranteed to be unique (within PAS analysis)
+        sample_name_to_uuid = {s["sample_name"]: s["id"] for s in samples}
+
+        msruns = self.find_msruns(sample_ids=[s["id"] for s in samples])
+        msrunid_to_info = {msrun["Run"]: msrun for msrun in msruns}
 
         # 2. Get search results
-        # pull the np/panel file, or report.tsv for precursor mode
+        # pull the np/panel file, or the relevant columns from the report.tsv for precursor mode
+        columns = None
+        if analyte_type == "precursor" and rollup == "np":
+            columnsExperiment = ["Run"]
+            columnsProtein = [
+                "Protein.Group",
+            ]
+            columnsPeptide = [
+                "Stripped.Sequence",
+            ]
+            columnsPrecursor = [
+                "Precursor.Id",
+                "Precursor.Charge",
+                "Precursor.Quantity",
+                "RT",
+                "iRT",
+                "IM",
+                "iIM",
+            ]
+            columnsQValue = [
+                "Q.Value",
+                "Protein.Q.Value",
+            ]
+            columns = [
+                *columnsExperiment,
+                *columnsProtein,
+                *columnsPeptide,
+                *columnsPrecursor,
+                *columnsQValue,
+            ]
         search_results = self.get_search_result(
             analysis_id=analysis_id,
             analyte_type=analyte_type,
             rollup=rollup,
+            columns=columns,
         )
+
         if analyte_type in ["protein", "peptide"]:
+            # set the intensity column based on norm_method and PAS analysis protocol version
             intensity_column = None
             if norm_method == "raw":
                 intensity_column = (
@@ -1532,140 +1576,171 @@ class _UnsupportedSDK(_SeerSDK):
                     raise ValueError(
                         "Pepcal normalized intensities not found in search results. This is only available with analyses processed with DIA-NN Seer Protocol v2.0 or later with the Seer Peptide Calibrant option enabled. \n Please retry using different norm_method, such as 'median'"
                     )
-
                 intensity_column = "PepCal Intensities Log10"
-
+            elif norm_method == "pepcal_batch":
+                if not (
+                    "PepCal Batch Intensities Log10" in search_results.columns
+                ):
+                    raise ValueError(
+                        "Pepcal normalized batch corrected intensities not found in search results. This is only available with analyses processed with DIA-NN Seer Protocol v2.0 or later with the Seer Peptide Calibrant option enabled. \n Please retry using different norm_method, such as 'median'"
+                    )
+                intensity_column = "PepCal Batch Intensities Log10"
             else:
                 raise ValueError(
                     f"norm_method = {norm_method} is not supported. Supported normalization methods are: raw, pepcal, engine, median, median80."
                 )
-            if rollup == "panel":
-                search_results.fillna({"Sample Name": ""}, inplace=True)
-                search_results["File Name"] = search_results[
-                    "Sample Name"
-                ].apply(
-                    lambda x: (
-                        os.path.basename(
-                            sample_to_msrun[sample_name_to_id[x]][
-                                "raw_file_path"
-                            ]
-                        ).split(".")[0]
-                        if x
-                        else None
-                    )
-                )
-            search_results["File Name"] = search_results["File Name"].apply(
-                lambda x: os.path.basename(x).split(".")[0] if x else None
-            )
 
             search_results["Intensity Log10"] = search_results[
                 intensity_column
             ]
 
-            # 3. Merge report to search results to get Q value and other properties
-            report = self.get_search_result(
-                analysis_id=analysis_id,
-                analyte_type="precursor",
-                rollup="np",
-            )
-            report["File Name"] = report["Run"]
-            report["Protein Group"] = report["Protein.Group"]
-
-            if analyte_type == "protein":
-                report["Protein Q Value"] = report["Protein.Q.Value"]
+            if rollup == "panel":
+                search_results.rename(
+                    columns={"Sample ID": "Sample UUID"}, inplace=True
+                )
+                search_results["Sample UUID"] = search_results[
+                    "Sample Name"
+                ].map(sample_name_to_uuid)
+                search_results["Sample ID"] = search_results[
+                    "Sample UUID"
+                ].map(sample_uuid_to_id)
+                experiment_columns = ["Sample UUID", "Sample ID"]
+
+                # analyte info is limited to the id in the panel rollup
+                if analyte_type == "protein":
+                    analyte_id_column = "Protein Group"
+                else:
+                    analyte_id_column = "Peptide"
+
+                analyte_columns = [analyte_id_column]
+                df = search_results
+            else:
+                # np rollup, extract basename without extension
+                path_to_msrunid = {
+                    path: filepath_to_msrunid(path)
+                    for path in search_results["File Name"].unique()
+                }
+                # strip path from the filename to allow merging with the precursor report
+                search_results["Run"] = search_results["File Name"].map(
+                    path_to_msrunid
+                )
 
-                report = report[
-                    ["File Name", "Protein Group", "Protein Q Value"]
-                ]
-                report.drop_duplicates(
-                    subset=["File Name", "Protein Group"], inplace=True
+                search_results["MsRun UUID"] = search_results["Run"].map(
+                    {k: v["id"] for k, v in msrunid_to_info.items()}
                 )
-                df = pd.merge(
-                    search_results,
-                    report,
-                    on=["File Name", "Protein Group"],
-                    how="left",
+                search_results["Sample ID"] = search_results["Run"].map(
+                    {k: v["sample_id"] for k, v in msrunid_to_info.items()}
+                )
+                search_results["Sample UUID"] = search_results["Run"].map(
+                    {k: v["sample_uuid"] for k, v in msrunid_to_info.items()}
                 )
-                included_columns = [
-                    "MsRun ID",
+                search_results["Nanoparticle"] = search_results["Run"].map(
+                    {k: v["nanoparticle"] for k, v in msrunid_to_info.items()}
+                )
+                experiment_columns = [
+                    "MsRun UUID",
+                    "Run",
+                    "Nanoparticle",
+                    "Sample UUID",
                     "Sample ID",
-                    "Protein Group",
-                    "Intensity Log10",
-                    "Protein Q Value",
                 ]
 
-            else:
-                report["Peptide"] = report["Stripped.Sequence"]
-                #  If analyte_type is peptide, attach retention time (RT, iRT)
-                report = report[["File Name", "Peptide", "RT", "iRT"]]
-                report.drop_duplicates(
-                    subset=["File Name", "Peptide"], inplace=True
+                # Merge report to search results to get Q value and other properties
+                if analyte_type == "protein":
+                    columns = ["Run", "Protein.Group", "Protein.Q.Value"]
+                elif analyte_type == "peptide":
+                    columns = ["Run", "Stripped.Sequence", "Protein.Q.Value"]
+                analytes = self.get_search_result(
+                    analysis_id=analysis_id,
+                    analyte_type="precursor",
+                    rollup="np",
+                    columns=columns,
+                )
+                # pandas Dataframe.rename() default behavior is to ignore the columns that do not exist in the data frame.
+                analytes.rename(
+                    columns={
+                        "Protein.Group": "Protein Group",
+                        "Protein.Q.Value": "Protein Q Value",
+                        "Stripped.Sequence": "Peptide",
+                    },
+                    inplace=True,
+                )
+
+                if analyte_type == "protein":
+                    analyte_id_column = "Protein Group"
+                    analyte_columns = [
+                        analyte_id_column,
+                        "Protein Q Value",
+                    ]
+
+                else:
+                    analyte_id_column = "Peptide"
+                    analyte_columns = [analyte_id_column]
+                # endif analyte_type
+
+                analytes.drop(
+                    columns=[
+                        col
+                        for col in analytes.columns
+                        if col != "Run" and col not in analyte_columns
+                    ],
+                    inplace=True,
+                )
+                analytes.drop_duplicates(
+                    subset=["Run", analyte_id_column], inplace=True
                 )
                 df = pd.merge(
                     search_results,
-                    report,
-                    on=["File Name", "Peptide"],
+                    analytes,
+                    on=["Run", analyte_id_column],
                     how="left",
+                    validate="one_to_one",
                 )
-                included_columns = [
-                    "MsRun ID",
-                    "Sample ID",
-                    "Peptide",
-                    "Protein Group",
-                    "Intensity Log10",
-                    "RT",
-                    "iRT",
-                ]
-            # endif
 
-            if rollup == "np":
-                included_columns.insert(
-                    included_columns.index("Sample ID") + 1, "Nanoparticle"
-                )
+            df = df[experiment_columns + analyte_columns + ["Intensity Log10"]]
 
-            df["MsRun ID"] = df["File Name"].apply(
-                lambda x: (
-                    file_to_msrun[x]["id"] if x in file_to_msrun else None
-                )
-            )
-            df["Sample ID"] = df["File Name"].apply(
-                lambda x: (
-                    file_to_msrun[x]["sample_id"]
-                    if x in file_to_msrun
-                    else None
-                )
-            )
-            df = df[included_columns]
-            df.columns = [title_case_to_snake_case(x) for x in df.columns]
-            return df
         else:
             # precursor
             # working only in report.tsv
-            search_results["Intensity"] = search_results["Precursor.Quantity"]
-            search_results["MsRun ID"] = search_results["Run"].apply(
-                lambda x: (
-                    file_to_msrun[x]["id"] if x in file_to_msrun else None
+            if norm_method != "raw":
+                raise ValueError(
+                    "For precursor analyte type, only 'raw' norm_method is supported."
                 )
+
+            search_results["MsRun UUID"] = search_results["Run"].map(
+                {k: v["id"] for k, v in msrunid_to_info.items()}
             )
-            search_results["Sample ID"] = search_results["Run"].apply(
-                lambda x: (
-                    file_to_msrun[x]["sample_id"]
-                    if x in file_to_msrun
-                    else None
-                )
+            search_results["Sample ID"] = search_results["Run"].map(
+                {k: v["sample_id"] for k, v in msrunid_to_info.items()}
+            )
+            search_results["Sample UUID"] = search_results["Sample ID"].map(
+                sample_id_to_uuid
             )
-            search_results["Protein Group"] = search_results["Protein.Group"]
-            search_results["Peptide"] = search_results["Stripped.Sequence"]
-            search_results["Charge"] = search_results["Precursor.Charge"]
-            search_results["Precursor Id"] = search_results["Precursor.Id"]
-            search_results["Precursor Q Value"] = search_results["Q.Value"]
-            search_results["Protein Q Value"] = search_results[
-                "Protein.Q.Value"
+            search_results["Nanoparticle"] = search_results["Run"].map(
+                {k: v["nanoparticle"] for k, v in msrunid_to_info.items()}
+            )
+            experiment_columns = [
+                "MsRun UUID",
+                "Run",
+                "Nanoparticle",
+                "Sample UUID",
+                "Sample ID",
             ]
 
-            included_columns = [
-                "MsRun ID",
-                "Sample ID",
+            search_results.rename(
+                columns={
+                    "Protein.Group": "Protein Group",
+                    "Stripped.Sequence": "Peptide",
+                    "Precursor.Charge": "Charge",
+                    "Precursor.Id": "Precursor Id",
+                    "Q.Value": "Precursor Q Value",
+                    "Protein.Q.Value": "Protein Q Value",
+                    "Precursor.Quantity": "Intensity",
+                },
+                inplace=True,
+            )
+
+            analyte_columns = [
                 "Protein Group",
                 "Protein Q Value",
                 "Peptide",
@@ -1678,10 +1753,13 @@ class _UnsupportedSDK(_SeerSDK):
                 "IM",
                 "iIM",
             ]
-            df = search_results[included_columns]
-            df.columns = [title_case_to_snake_case(x) for x in df.columns]
+            df = pd.DataFrame(
+                search_results[experiment_columns + analyte_columns]
+            )
 
-            return df
+        df.columns = [title_case_to_snake_case(x) for x in df.columns]
+
+        return df
 
     def get_search_data_analytes(self, analysis_id: str, analyte_type: str):
         if analyte_type not in ["protein", "peptide", "precursor"]:
@@ -1697,10 +1775,6 @@ class _UnsupportedSDK(_SeerSDK):
             analysis_id=analysis_id, analyte_type="protein", rollup="np"
         )
 
-        report_results = self.get_search_result(
-            analysis_id=analysis_id, analyte_type="precursor", rollup="np"
-        )
-
         search_results = search_results[
             [
                 "Protein Group",
@@ -1712,18 +1786,87 @@ class _UnsupportedSDK(_SeerSDK):
             ]
         ]
         search_results.drop_duplicates(subset=["Protein Group"], inplace=True)
-        report_results["Protein Group"] = report_results["Protein.Group"]
-        report_results["Peptide"] = report_results["Stripped.Sequence"]
 
-        if analyte_type == "protein":
-            report_results = report_results[
+        # 2. fetch precursor report to extract analyte-specific details
+        columnsPG = [
+            "Protein.Group",
+        ]
+        columnsPeptide = [
+            "Protein.Ids",
+            "Stripped.Sequence",
+            "Proteotypic",
+        ]
+        columnsPrecursor = [
+            "Precursor.Id",
+            "Precursor.Charge",
+            "Precursor.Quantity",
+            "Modified.Sequence",
+        ]
+        columnsPGQValue = [
+            "Global.PG.Q.Value",
+            "Lib.PG.Q.Value",
+        ]
+        columnsPrecursorQValue = [
+            "Global.Q.Value",
+            "Lib.Q.Value",
+        ]
+        columns = [
+            *columnsPG,
+            *columnsPGQValue,
+        ]
+        if analyte_type == "peptide":
+            columns += [*columnsPeptide]
+        elif analyte_type == "precursor":
+            columns += [
+                *columnsPeptide,
+                *columnsPrecursor,
+                *columnsPrecursorQValue,
+            ]
+        report_results = self.get_search_result(
+            analysis_id=analysis_id,
+            analyte_type="precursor",
+            rollup="np",
+            columns=columns,
+        )
+        report_results.rename(
+            columns={
+                "Protein.Group": "Protein Group",
+                "Stripped.Sequence": "Peptide",
+                "Modified.Sequence": "Modified.Peptide",
+            },
+            inplace=True,
+        )
+
+        # function to fix the potential bug, where different precursors
+        # of the same peptide map to different protein groups
+        def fix_peptide_to_protein_group_assignment(
+            df: pd.DataFrame,
+        ) -> pd.DataFrame:
+            # for each peptide, sort protein groups by confidence
+            df = df.sort_values(
                 [
-                    "Protein Group",
-                    "Protein.Ids",
+                    "Peptide",
                     "Global.PG.Q.Value",
                     "Lib.PG.Q.Value",
+                    "Protein Group",
                 ]
-            ]
+            )
+
+            # broadcast the best protein group across all rows with the same peptide
+            # to fix the potential bug, where different precursors of the same peptide
+            # map to different protein groups
+            for col in [
+                "Protein Group",
+                "Protein.Ids",
+                "Protein.Names",
+                "Genes",
+            ]:
+                if col in df.columns:
+                    df[col] = df.groupby("Peptide")[col].transform("first")
+
+            return df
+
+        if analyte_type == "protein":
             report_results.drop_duplicates(
                 subset=["Protein Group"], inplace=True
             )
@@ -1734,25 +1877,23 @@ class _UnsupportedSDK(_SeerSDK):
                 how="left",
             )
         elif analyte_type == "peptide":
-            peptide_results = self.get_search_result(
-                analysis_id=analysis_id, analyte_type="peptide", rollup="np"
-            )
-            peptide_results = peptide_results[["Peptide", "Protein Group"]]
-            search_results = pd.merge(
-                peptide_results,
-                search_results,
-                on=["Protein Group"],
-                how="left",
-            )
-
-            report_results = report_results[
-                ["Peptide", "Protein.Ids", "Protein.Group"]
+            search_results = search_results[
+                [
+                    "Protein Group",
+                    "Protein Names",
+                    "Gene Names",
+                ]
             ]
+            report_results.drop_duplicates(inplace=True)
+            report_results = fix_peptide_to_protein_group_assignment(
+                report_results
+            )
             report_results.drop_duplicates(subset=["Peptide"], inplace=True)
+
             df = pd.merge(
-                search_results,
                 report_results,
-                on=["Peptide"],
+                search_results,
+                on=["Protein Group"],
                 how="left",
             )
         else:
@@ -1762,66 +1903,25 @@ class _UnsupportedSDK(_SeerSDK):
                     "Protein Group",
                     "Protein Names",
                     "Gene Names",
-                    "Biological Process",
-                    "Molecular Function",
-                    "Cellular Component",
                 ]
             ]
-            search_results.drop_duplicates(
-                subset=["Protein Group"], inplace=True
+            report_results.drop_duplicates(inplace=True)
+
+            report_results = fix_peptide_to_protein_group_assignment(
+                report_results
             )
-            report_results = report_results[
-                [
-                    "Precursor.Id",
-                    "Precursor.Charge",
-                    "Peptide",
-                    "Protein Group",
-                    "Protein.Ids",
-                    "Protein.Names",
-                    "Genes",
-                    "First.Protein.Description",
-                    "Modified.Sequence",
-                    "Proteotypic",
-                    "Global.Q.Value",
-                    "Global.PG.Q.Value",
-                    "Lib.Q.Value",
-                    "Lib.PG.Q.Value",
-                ]
-            ]
             report_results.drop_duplicates(
-                subset=["Protein Group"], inplace=True
+                subset=["Peptide", "Modified.Peptide", "Precursor.Charge"],
+                inplace=True,
             )
+
             df = pd.merge(
                 report_results,
                 search_results,
                 on=["Protein Group"],
                 how="left",
             )
-            df = df[
-                [
-                    "Precursor.Id",
-                    "Precursor.Charge",
-                    "Peptide",
-                    "Protein Group",
-                    "Protein.Ids",
-                    "Protein.Names",
-                    "Genes",
-                    "First.Protein.Description",
-                    "Modified.Sequence",
-                    "Proteotypic",
-                    "Global.Q.Value",
-                    "Global.PG.Q.Value",
-                    "Lib.Q.Value",
-                    "Lib.PG.Q.Value",
-                    "Gene Names",
-                    "Biological Process",
-                    "Molecular Function",
-                    "Cellular Component",
-                ]
-            ]
-            df.rename(
-                columns={"Modified.Sequence": "Modified.Peptide"}, inplace=True
-            )
         # endif
         df.columns = [title_case_to_snake_case(x) for x in df.columns]
+
         return df

{seer_pas_sdk-1.1.1.dist-info → seer_pas_sdk-1.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seer-pas-sdk
-Version: 1.1.1
+Version: 1.2.1
 Summary: SDK for Seer Proteograph Analysis Suite (PAS)
 Author-email: Ryan Sun <rsun@seer.bio>
 License: 

{seer_pas_sdk-1.1.1.dist-info → seer_pas_sdk-1.2.1.dist-info}/RECORD

@@ -1,19 +1,19 @@
 seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
 seer_pas_sdk/auth/__init__.py,sha256=e_eM4jJnnyKUdg4Nggzi9ypt2MLWcEJ8CmCPkUaQDSs,23
 seer_pas_sdk/auth/auth.py,sha256=_SI5CdEkfqfr4o5BQ79BuPbxGeI9p7tqxJd7mUqSAkI,8854
-seer_pas_sdk/common/__init__.py,sha256=8r-xF0alzIdCRdtpQCWKs6pQFrOi9KYnO7EwP8Pm94A,23475
+seer_pas_sdk/common/__init__.py,sha256=VbtcWOt9_jR5NfETtYTqcUXII98Jj5sphr3lLSdIzdg,24445
 seer_pas_sdk/common/errors.py,sha256=4HFORWnaQQCMXRE8kwdsJWvQRB_3KFEZ7yMb391e4gA,142
 seer_pas_sdk/common/groupanalysis.py,sha256=DxB-gbQfYzl7p9MTYWDIqghcH-IeakzdYdrRZrlIHek,1730
 seer_pas_sdk/core/__init__.py,sha256=rxbKgg-Qe24OaxX2zyHHYPYgDCTEKE_-41bB2wvpvL4,25
-seer_pas_sdk/core/sdk.py,sha256=OKN7z11hm0Uzx-1yO3YxiN4OCar_4tjDwpKQBjzXeD0,160092
-seer_pas_sdk/core/unsupported.py,sha256=SicgUHz1j-aLfcTvkWiSDMAm9D58VEv0YX-3PGQybec,69047
+seer_pas_sdk/core/sdk.py,sha256=0ukg287lsjlSNoV0WqFbiPMURhVogsy_sTR7gg1fr9Q,161512
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