SeerSDK

SeerSDK(username, password, instance='US', tenant=None)

Object exposing SDK methods. Requires a username and password; the optional instance param denotes the instance of PAS (defaults to “US”).

Examples

>>> from seer_pas_sdk import SeerSDK
>>> USERNAME = "test"
>>> PASSWORD = "test-password"
>>> INSTANCE = "EU"
>>> seer_sdk = SeerSDK(USERNAME, PASSWORD, INSTANCE)

Methods

Name	Description
analysis_complete	Returns the status of the analysis with the given id.
download_ms_data_files	Downloads all MS data files for paths passed in the params to the specified download path.
download_search_output_file	Given an analysis id and a analysis result filename, this function downloads the file to the specified path.
get_active_tenant	Fetches the active tenant for the authenticated user.
get_active_tenant_id	Fetches the active tenant ID for the authenticated user.
get_active_tenant_name	Fetches the active tenant name for the authenticated user.
get_all_volcano_plot_data	Get all volcano plot data for a given analysis.
get_analyses	Returns a list of analyses objects for the authenticated user. If no id is provided, returns all analyses for the authenticated user.
get_analysis_hierarchical_clustering	Get hierarchical clustering data for given analyses and samples.
get_analysis_pca_data	Get PCA data for given analyses and samples formatted in a DataFrame or a dictionary.
get_analysis_protocol_fasta
get_analysis_protocols	Fetches a list of analysis protocols for the authenticated user. If no analysis_protocol_id is provided, returns all analysis protocols for the authenticated user. If analysis_protocol_name (and no analysis_protocol_id) is provided, returns the analysis protocol with the given name, provided it exists.
get_analysis_result	Given an analysis_id, this function returns all relevant analysis data files in form of downloadable content, if applicable.
get_analysis_result_files	Given an analysis id and a list of file names, this function returns the file in form of downloadable content, if applicable.
get_analysis_result_peptide_data	Given an analysis id, this function returns the peptide data for the analysis.
get_analysis_result_protein_data	Given an analysis id, this function returns the protein data for the analysis.
get_box_plot_data	Get box plot data for given analyses and samples formatted in a DataFrame or a dictionary.
get_cluster_heatmap_data	Get cluster heatmap data for the given analysis.
get_enrichment_plot	Get enrichment plot data for a given analysis ID.
get_group_analysis	Returns the list of group analysis objects for the given analysis id, provided they exist.
get_msruns	Fetches MS data files for passed in sample_ids (provided they are valid and contain relevant files) for an authenticated user.
get_peptide_results_table	Fetches the peptide results table for a given analysis ID or analysis name.
get_plates	Fetches a list of plates for the authenticated user. If no plate_id is provided, returns all plates for the authenticated user. If plate_id is provided, returns the plate with the given plate_id, provided it exists.
get_ppi_network_data	Get PPI network data for given significant protein groups.
get_projects	Fetches a list of projects for the authenticated user. If no project_id is provided, returns all projects for the authenticated user. If project_id is provided, returns the project with the given project_id, provided it exists.
get_protein_results_table	Fetches the protein results table for a given analysis ID or analysis name.
get_samples	Fetches a list of samples for the authenticated user with relation to a specified plate, project, or analysis. If no parameters are provided, returns all samples for the authenticated user. If plate_id or project_id is provided, returns samples associated with that plate or project. If analysis_id or analysis_name is provided, returns samples associated with that analysis.
get_search_result	Load one of the files available via the “Download result files” button on the PAS UI.
get_search_result_file_url	Given an analysis id and a analysis result filename, this function returns the signed URL for the file.
get_spaces	Fetches a list of spaces for the authenticated user.
get_user_tenant	Fetches the tenant metadata for the authenticated user.
get_volcano_plot_data	Get volcano plot data for a given analysis ID.
group_analysis_results	Returns the group analysis data for the given analysis id, provided it exists.
list_ms_data_files	Lists all the MS data files in the given folder as long as the folder path passed in the params is valid.
list_search_result_files	Given an analysis id, this function returns a list of files associated with the analysis.
list_tenants	Lists the institution names and the tenant ids for the authenticated user.
switch_tenant	Switches the tenant for the authenticated user.

analysis_complete

SeerSDK.analysis_complete(analysis_id)

Returns the status of the analysis with the given id.

Parameters

Name	Type	Description	Default
analysis_id	str	The analysis id.	required

Returns

Name	Type	Description
res	dict	A dictionary containing the status of the analysis.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> seer_sdk.analysis_complete("YOUR_ANALYSIS_ID_HERE")
>>> {
        "status": "SUCCEEDED"
    }

download_ms_data_files

SeerSDK.download_ms_data_files(paths, download_path, space=None)

Downloads all MS data files for paths passed in the params to the specified download path.

Parameters

Name	Type	Description	Default
paths	list[str]	List of paths to download.	required
download_path	str	Path to download the files to.	required
space	str	ID of the user group to which the files belongs, defaulted to None.	None

Returns

Name	Type	Description
message	dict[str, str]	Contains the ‘message’ whether the files were downloaded or not.

download_search_output_file

SeerSDK.download_search_output_file(analysis_id, filename, download_path='')

Given an analysis id and a analysis result filename, this function downloads the file to the specified path.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis for which the data is to be fetched.	required
filename	str	Name of the file to be fetched. Files can be case insensitive and without file extensions.	required
download_path	str	String flag denoting where the user wants the files downloaded. Can be local or absolute as long as the path is valid.	''

Returns

Name	Type	Description
	None	Downloads the file to the specified path.

get_active_tenant

SeerSDK.get_active_tenant()

Fetches the active tenant for the authenticated user.

Returns

Name	Type	Description
tenant	dict[str, str]	Tenant metadata for the authenticated user containing “institution” and “tenantId” keys.

get_active_tenant_id

SeerSDK.get_active_tenant_id()

Fetches the active tenant ID for the authenticated user.

Returns

Name	Type	Description
tenant_id	str	Tenant ID for the authenticated user.

get_active_tenant_name

SeerSDK.get_active_tenant_name()

Fetches the active tenant name for the authenticated user.

Returns

Name	Type	Description
tenant	str	Tenant name for the authenticated user.

get_all_volcano_plot_data

SeerSDK.get_all_volcano_plot_data(analysis_id, box_plot=False)

Get all volcano plot data for a given analysis.

Args: analysis_id (str): ID of the analysis. box_plot (bool, optional): Mark true to include box plot data in the return object. Defaults to False.

Returns: dict[str, pd.DataFrame]: A dictionary containing the volcano plot and optionally box plot data for each group analysis.

get_analyses

SeerSDK.get_analyses(
    analysis_id=None,
    folder_id=None,
    show_folders=True,
    analysis_only=True,
    project_id=None,
    plate_name=None,
    as_df=False,
    **kwargs,
)

Returns a list of analyses objects for the authenticated user. If no id is provided, returns all analyses for the authenticated user. Search parameters may be passed in as keyword arguments to filter the results. Acceptable values are ‘analysis_name’, ‘folder_name’, ‘description’, ‘notes’, or ‘number_msdatafile’. Only search on a single field is supported.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis to be fetched, defaulted to None.	None
folder_id	str	ID of the folder to be fetched, defaulted to None.	None
show_folders	bool	Mark True if folder contents are to be returned in the response, i.e. recursive search, defaulted to True. Will be disabled if an analysis id is provided.	True
analysis_only	bool	Mark True if only analyses objects are to be returned in the response, defaulted to True. If marked false, folder objects will also be included in the response.	True
project_id	str	ID of the project to be fetched, defaulted to None.	None
plate_name	str	Name of the plate to be fetched, defaulted to None.	None
as_df	bool	whether the result should be converted to a DataFrame, defaulted to False.	False
**kwargs	dict	Search keyword parameters to be passed in. Acceptable values are ‘analysis_name’, ‘folder_name’, ‘analysis_protocol_name’, ‘description’, ‘notes’, or ‘number_msdatafile’.	{}

Returns

Name	Type	Description
analyses	list[dict]	Contains a list of analyses objects for the authenticated user.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> seer_sdk.get_analyses()
>>> [
        {id: "YOUR_ANALYSIS_ID_HERE", ...},
        {id: "YOUR_ANALYSIS_ID_HERE", ...},
        {id: "YOUR_ANALYSIS_ID_HERE", ...}
    ]

>>> seer_sdk.get_analyses("YOUR_ANALYSIS_ID_HERE")
>>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]

>>> seer_sdk.get_analyses(folder_name="YOUR_FOLDER_NAME_HERE")
>>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]

>>> seer_sdk.get_analyses(analysis_name="YOUR_ANALYSIS")
>>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]

>>> seer_sdk.get_analyses(description="YOUR_DESCRIPTION")
>>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]

get_analysis_hierarchical_clustering

SeerSDK.get_analysis_hierarchical_clustering(
    analysis_ids,
    sample_ids=[],
    hide_control=False,
)

Get hierarchical clustering data for given analyses and samples. Args: analysis_ids (list[str]): IDs of the analyses. sample_ids (list[str], optional): IDs of the samples. hide_control (bool, optional): Mark true if controls are to be excluded. Defaults to False. raw_data (bool, optional): Mark true if raw data should be returned. Defaults to True. Raises: ValueError: No analysis IDs provided. ValueError: No sample IDs provided. ValueError: Response status code is not 200. Returns: dict Hierarchical clustering data returned by the API.

get_analysis_pca_data

SeerSDK.get_analysis_pca_data(
    analysis_ids,
    type,
    sample_ids=[],
    hide_control=False,
    as_df=False,
)

Get PCA data for given analyses and samples formatted in a DataFrame or a dictionary. Args: analysis_ids (list[str]): IDs of the analyses of interest. type (str): Type of data to be fetched. Must be either ‘protein’ or ‘peptide’. sample_ids (list[str], optional): IDs of the samples of interest. hide_control (bool, optional): Mark true if controls are to be excluded. Defaults to False. as_df (bool, optional): whether the result should be converted to a DataFrame. Defaults to False. Raises: ValueError: No analysis IDs provided. ValueError: No sample IDs provided. ValueError: Invalid type parameter provided. ServerError: Could not fetch PCA data. Returns: A dictionary with the following keys: - x_contribution_ratio (float): Proportion of variance explained by the x-axis. - y_contribution_ratio (float): Proportion of variance explained by the y-axis. - data (list[dict] | pd.DataFrame): A list of dictionaries or a dataframe with each row containing the following keys/columns: - sample_name (str): Name of the sample. - plate_name (str): Name of the plate. - sample_id (int): ID of the sample. - condition (str): Condition. - PC1 (float): X-value of the PCA point. - PC2 (float): Y-value of the PCA point. - custom_* (str): Custom fields. Included if meaningful, i.e., not null, in the data.

Examples

>>> from seer_pas_sdk import *
>>> sdk = SeerSDK()
>>> sdk.get_analysis_pca_data(
        analysis_ids=["analysis_id"],
        sample_ids=["sample_id"],
        type="protein",
        hide_control=False
    )

get_analysis_protocol_fasta

SeerSDK.get_analysis_protocol_fasta(analysis_id, download_path=None)

get_analysis_protocols

SeerSDK.get_analysis_protocols(
    analysis_protocol_name=None,
    analysis_protocol_id=None,
    as_df=False,
)

Fetches a list of analysis protocols for the authenticated user. If no analysis_protocol_id is provided, returns all analysis protocols for the authenticated user. If analysis_protocol_name (and no analysis_protocol_id) is provided, returns the analysis protocol with the given name, provided it exists.

Parameters

Name	Type	Description	Default
analysis_protocol_id	str	ID of the analysis protocol to be fetched, defaulted to None.	None
analysis_protocol_name	str	Name of the analysis protocol to be fetched, defaulted to None.	None
as_df	bool	whether the result should be converted to a DataFrame, defaulted to False.	False

Returns

Name	Type	Description
protocols	list[dict]	List of analysis protocol objects for the authenticated user.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> seer_sdk.get_analysis_protocols()
>>> [
        { "id": ..., "analysis_protocol_name": ... },
        { "id": ..., "analysis_protocol_name": ... },
        ...
    ]

>>> seer_sdk.get_analysis_protocols(name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
>>> [{ "id": ..., "analysis_protocol_name": ... }]

>>> seer_sdk.get_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE")
>>> [{ "id": ..., "analysis_protocol_name": ... }]

>>> seer_sdk.get_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE", name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")

>>> [{ "id": ..., "analysis_protocol_name": ... }] # in this case the id would supersede the inputted name.

get_analysis_result

SeerSDK.get_analysis_result(analysis_id, download_path='', diann_report=False)

Given an analysis_id, this function returns all relevant analysis data files in form of downloadable content, if applicable.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis for which the data is to be fetched.	required
download_path	str	String flag denoting where the user wants the files downloaded. Can be local or absolute as long as the path is valid. Defaults to an empty string.	''
diann_report	bool	Boolean flag denoting whether the user wants the DIANN report to be included in the response. Defaults to False.	False

Returns

Name	Type	Description
links	dict	Contains dataframe objects for the analysis_id, given that the analysis has been complete.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()

>>> seer_sdk.get_analysis_result("YOUR_ANALYSIS_ID_HERE")
>>> {
        "peptide_np": <peptide_np dataframe object>,
        "peptide_panel": <peptide_panel dataframe object>,
        "protein_np": <protein_np dataframe object>,
        "protein_panel": <protein_panel dataframe object>
    }

>>> seer_sdk.get_analysis_result("YOUR_DIANN_ANALYSIS_ID_HERE")
>>> {
        "peptide_np": <peptide_np dataframe object>,
        "peptide_panel": <peptide_panel dataframe object>,
        "protein_np": <protein_np dataframe object>,
        "protein_panel": <protein_panel dataframe object>,
        "diann_report": <report.tsv dataframe object>
    }

>>> seer_sdk.get_analysis_result("YOUR_ANALYSIS_ID_HERE", download_path="/Users/Downloads")
>>> { "status": "Download complete." }

get_analysis_result_files

SeerSDK.get_analysis_result_files(
    analysis_id,
    filenames,
    download_path='',
    protein_all=False,
    peptide_all=False,
)

Given an analysis id and a list of file names, this function returns the file in form of downloadable content, if applicable.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis for which the data is to be fetched.	required
filenames	list	List of filenames to be fetched. Only csv and tsv files are supported.	required
download_path	str	String flag denoting where the user wants the files downloaded. Can be local or absolute as long as the path is valid. Defaults to an empty string.	''
protein_all	bool	Boolean flag denoting whether the user wants the default protein data. Defaults to False.	False
peptide_all	bool	Boolean flag denoting whether the user wants the default peptide data. Defaults to False.	False

Returns

Name	Type	Description
links	dict[str, pd.DataFrame]	Contains dataframe objects for the requested files. If a filename is not found, it is skipped.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> analysis_id = "YOUR_ANALYSIS_ID_HERE"
>>> filenames = ["protein_np.tsv", "peptide_np.tsv"]
>>> seer_sdk.get_analysis_result_files(analysis_id, filenames)
    {
        "protein_np.tsv": <protein_np dataframe object>,
        "peptide_np.tsv": <peptide_np dataframe object>
    }
>>> seer_sdk.get_analysis_result_files(analysis_id, [], protein_all=True, peptide_all=True)
    {
        "protein_np.tsv": <protein_np dataframe object>,
        "protein_panel.tsv": <protein_panel dataframe object>,
        "peptide_np.tsv": <peptide_np dataframe object>,
        "peptide_panel.tsv": <peptide_panel dataframe object>
    }
>>> seer_sdk.get_analysis_result_files(analysis_id, ["report.tsv"], download_path="/Users/Downloads")
    { "report.tsv": <report.tsv dataframe object> }

get_analysis_result_peptide_data

SeerSDK.get_analysis_result_peptide_data(analysis_id, link=False, peptide=None)

Given an analysis id, this function returns the peptide data for the analysis.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis for which the data is to be fetched.	required
link	bool	Boolean flag denoting whether the user wants the default peptide data. Defaults to False.	False
peptide	str	Peptide sequence to filter dataframe results. Defaults to None.	None

get_analysis_result_protein_data

SeerSDK.get_analysis_result_protein_data(analysis_id, link=False, pg=None)

Given an analysis id, this function returns the protein data for the analysis.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis for which the data is to be fetched.	required
link	bool	Boolean flag denoting whether the user wants the default protein data. Defaults to False.	False
pg	str	Protein group ID to filter dataframe results. Defaults to None.	None

get_box_plot_data

SeerSDK.get_box_plot_data(
    analysis_id,
    group_analysis_id=None,
    feature_ids=[],
    show_significant_only=False,
    as_df=False,
    volcano_plot=False,
    cached=False,
)

Get box plot data for given analyses and samples formatted in a DataFrame or a dictionary.

Args: analysis_id (str): ID of the analysis. feature_ids (list[str], optional): Filter result object to a set of ids. Defaults to []. show_significant_only (bool, optional): Mark true if only significant results are to be returned. Defaults to False. as_df (bool, optional): whether the result should be converted to a DataFrame. Defaults to False. volcano_plot (bool, optional): Mark true to include the volcano plot data in the return object. Defaults to False. cached (bool, optional): Mark true to return volcano plot data as a VolcanoPlotBuilder object. No effect if volcano_plot flag is marked false. Defaults to False.

Raises: ValueError: Invalid feature type. Must be either ‘protein’ or ‘peptide’. ServerError: Could not fetch box plot data.

Returns: list[dict] | pd.DataFrame : A list of dictionaries or a dataframe with each row containing the following keys/columns: ‘proteinId’, ‘intensity’, ‘sampleName’, ‘sampleId’, ‘condition’,‘gene’

get_cluster_heatmap_data

SeerSDK.get_cluster_heatmap_data(
    analysis_id,
    grouping,
    groups,
    contrasts,
    stat_test,
    feature_type,
    significant_pgs=[],
)

Get cluster heatmap data for the given analysis.

Args: analysis_id (str): ID of the analysis grouping (str): Category of sample groups groups (_List[str]): sample groups contrasts (_List[_Tuple[int, …]]): Indicate which groups are compared against each other. e.g. [(0, 1, -1, 0), (1, 0, 0, -1)] stat_test (str): Statistical test to be used feature_type (str): Type of feature to be used, either proteingroup or peptide significant_pgs (_List[str], optional): significant protein group IDs. Defaults to [].

Raises: ValueError: “Feature type must be either ‘proteingroup’ or ‘peptide’.” ValueError: “Stat test must be either ‘ttest’ or ‘wilcoxon’.” ValueError: Invalid contrast value. ValueError: Server error

Returns: dict: the response object clusterProtein: List of protein clusters clusters: indexes: list[int], List of indexes height: int, Height of the cluster children: list[dict] | None, Children of the cluster clusterSample: List of sample clusters clusters: indexes: list[int], List of indexes height: int, Height of the cluster children: list[dict] | None, Children of the cluster data: List of data

get_enrichment_plot

SeerSDK.get_enrichment_plot(
    analysis_id,
    significant_pgs,
    summarize_output=False,
    exclude_singleton=False,
    cutoff=None,
    species=None,
)

Get enrichment plot data for a given analysis ID.

Args: analysis_id (str): ID of the analysis. significant_pgs (_List[str]): List of significant protein/peptide groups. summarize_output (bool, optional): Summarize the output. Defaults to False. exclude_singleton (bool, optional): Exclude singleton values. Defaults to False. cutoff (float, optional): Cutoff value for the p-value to determine significance. Defaults to None. species (str, optional): Species to filter the data by. Defaults to None.

Raises: ServerError - could not fetch enrichment plot data.

Returns: dict: A dictionary containing the enrichment plot data.

get_group_analysis

SeerSDK.get_group_analysis(analysis_id, group_analysis_id=None, **kwargs)

Returns the list of group analysis objects for the given analysis id, provided they exist.

Parameters

Name	Type	Description	Default
analysis_id	str	The analysis id.	required
group_analysis_id	str	The group analysis id, defaulted to None. If provided, the function will return the group analysis object for the given group analysis id.	None
**kwargs	dict	Search keyword parameters to be passed in. Acceptable values are ‘name’ or ‘description’.	{}

Returns

Name	Type	Description
res	list[dict]	A list of dictionaries containing the group analysis objects.

get_msruns

SeerSDK.get_msruns(sample_ids, as_df=False)

Fetches MS data files for passed in sample_ids (provided they are valid and contain relevant files) for an authenticated user.

The function returns a dict containing DataFrame objects if the df flag is passed in as True, otherwise a nested dict object is returned instead.

Parameters

Name	Type	Description	Default
sample_ids	list	List of unique sample IDs.	required
as_df	bool	whether the result should be converted to a DataFrame, defaulted to False.	False

Returns

Name	Type	Description
res	list[dict] or DataFrame	List/DataFrame of plate objects for the authenticated user.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> sample_ids = ["812139c0-15e0-11ee-bdf1-bbaa73585acf", "803e05b0-15e0-11ee-bdf1-bbaa73585acf"]

>>> seer_sdk.get_msruns(sample_ids)
>>> [
    {"id": "SAMPLE_ID_1_HERE" ... },
    {"id": "SAMPLE_ID_2_HERE" ... }
]

>>> seer_sdk.get_msruns(sample_ids, as_df=True)
>>>                                      id  ... gradient
    0  81c6a180-15e0-11ee-bdf1-bbaa73585acf  ...     None
    1  816a9ed0-15e0-11ee-bdf1-bbaa73585acf  ...     None

[2 rows x 26 columns]

get_peptide_results_table

SeerSDK.get_peptide_results_table(
    analysis_id=None,
    analysis_name=None,
    grouping='condition',
    as_df=False,
)

Fetches the peptide results table for a given analysis ID or analysis name.

Args: analysis_id (str, optional): id of the analysis. Defaults to None. analysis_name (str, optional): name of the analysis. Defaults to None. grouping (str, optional): group criteria of table results. Defaults to “condition”. as_df (bool, optional): whether the result should be converted to a DataFrame, defaulted to False.

Raises: ValueError: neither name or id were provided for an analysis. ServerError: the request to the server was not successful.

Returns: list[dict] | pd.DataFrame: data from the peptide results table.

get_plates

SeerSDK.get_plates(plate_id=None, plate_name=None, as_df=False)

Fetches a list of plates for the authenticated user. If no plate_id is provided, returns all plates for the authenticated user. If plate_id is provided, returns the plate with the given plate_id, provided it exists.

Parameters

Name	Type	Description	Default
plate_id	str	ID of the plate to be fetched, defaulted to None.	None
as_df	bool	whether the result should be converted to a DataFrame, defaulted to None.	False

Returns

Name	Type	Description
plates	list[dict] or DataFrame	List/DataFrame of plate objects for the authenticated user.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> seer_sdk.get_plates()
>>> [
        { "id": ... },
        { "id": ... },
        ...
    ]
>>> seer_sdk.get_plates(as_df=True)
>>>                                        id  ... user_group
    0    a7c12190-15da-11ee-bdf1-bbaa73585acf  ...       None
    1    8c3b1480-15da-11ee-bdf1-bbaa73585acf  ...       None
    2    6f158840-15da-11ee-bdf1-bbaa73585acf  ...       None
    3    1a8a2920-15da-11ee-bdf1-bbaa73585acf  ...       None
    4    7ab47f40-15d9-11ee-bdf1-bbaa73585acf  ...       None
    ..                                    ...  ...        ...
    935  8fa91c00-6621-11ea-96e3-d5a4dab4ebf6  ...       None
    936  53180b20-6621-11ea-96e3-d5a4dab4ebf6  ...       None
    937  5c31fe90-6618-11ea-96e3-d5a4dab4ebf6  ...       None
    938  5b05d440-6610-11ea-96e3-d5a4dab4ebf6  ...       None
    939  9872e3f0-544e-11ea-ad9e-1991e0725494  ...       None

>>> seer_sdk.get_plate_metadata(id="YOUR_PLATE_ID_HERE")
>>> [{ "id": ... }]

get_ppi_network_data

SeerSDK.get_ppi_network_data(significant_pgs, species=None)

Get PPI network data for given significant protein groups. Args: significant_pgs (_List[str]): Significant protein groups. species (str, optional): Species of interest. Defaults to None. Raises: ValueError: No significant protein groups provided. ValueError: Response status code is not 200. Returns: dict Response returned by the API.

get_projects

SeerSDK.get_projects(project_id=None, project_name=None, as_df=False)

Fetches a list of projects for the authenticated user. If no project_id is provided, returns all projects for the authenticated user. If project_id is provided, returns the project with the given project_id, provided it exists.

Parameters

Name	Type	Description	Default
project_id	str	Project ID of the project to be fetched, defaulted to None.	None
as_df	bool	whether the result should be converted to a DataFrame, defaulted to False.	False

Returns

Name	Type	Description
projects	list[dict] or DataFrame	DataFrame or list of project objects for the authenticated user.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> seer_sdk.get_projects()
>>> [
        { "project_name": ... },
        { "project_name": ... },
        ...
    ]

>>> seer_sdk.get_projects(as_df=True)
>>>                                        id  ... user_group
    0    a7c12190-15da-11ee-bdf1-bbaa73585acf  ...       None
    1    8c3b1480-15da-11ee-bdf1-bbaa73585acf  ...       None
    2    6f158840-15da-11ee-bdf1-bbaa73585acf  ...       None
    3    1a8a2920-15da-11ee-bdf1-bbaa73585acf  ...       None
    4    7ab47f40-15d9-11ee-bdf1-bbaa73585acf  ...       None
    ..                                    ...  ...        ...
    935  8fa91c00-6621-11ea-96e3-d5a4dab4ebf6  ...       None
    936  53180b20-6621-11ea-96e3-d5a4dab4ebf6  ...       None
    937  5c31fe90-6618-11ea-96e3-d5a4dab4ebf6  ...       None
    938  5b05d440-6610-11ea-96e3-d5a4dab4ebf6  ...       None
    939  9872e3f0-544e-11ea-ad9e-1991e0725494  ...       None

>>> seer_sdk.get_projects(id="YOUR_PROJECT_ID_HERE")
>>> [{ "project_name": ... }]

get_protein_results_table

SeerSDK.get_protein_results_table(
    analysis_id=None,
    analysis_name=None,
    grouping='condition',
    as_df=False,
)

Fetches the protein results table for a given analysis ID or analysis name.

Args: analysis_id (str, optional): id of the analysis. Defaults to None. analysis_name (str, optional): name of the analysis. Defaults to None. grouping (str, optional): group criteria of table result. Defaults to “condition”. as_df (bool, optional): . Defaults to False.

Raises: ValueError: neither name or id were provided for an analysis. ServerError: the request to the server was not successful.

Returns: list[dict] | pd.DataFrame: data from the protein results table.

get_samples

SeerSDK.get_samples(
    plate_id=None,
    project_id=None,
    analysis_id=None,
    analysis_name=None,
    as_df=False,
)

Fetches a list of samples for the authenticated user with relation to a specified plate, project, or analysis. If no parameters are provided, returns all samples for the authenticated user. If plate_id or project_id is provided, returns samples associated with that plate or project. If analysis_id or analysis_name is provided, returns samples associated with that analysis.

Parameters

Name	Type	Description	Default
plate_id	str	ID of the plate for which samples are to be fetched, defaulted to None.	None
project_id	str	ID of the project for which samples are to be fetched, defaulted to None.	None
analysis_id	str	ID of the analysis for which samples are to be fetched, defaulted to None.	None
analysis_name	str	Name of the analysis for which samples are to be fetched, defaulted to None.	None
as_df	bool	whether the result should be converted to a DataFrame, defaulted to False.	False

Returns

Name	Type	Description
samples	list[dict] or DataFrame	List/DataFrame of samples for the authenticated user.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()

>>> seer_sdk.get_samples(plate_id="7ec8cad0-15e0-11ee-bdf1-bbaa73585acf")
>>> [
        { "id": ... },
        { "id": ... },
        ...
    ]

>>> seer_sdk.get_samples(as_df=True)
>>>                                     id  ...      control
0     812139c0-15e0-11ee-bdf1-bbaa73585acf  ...
1     803e05b0-15e0-11ee-bdf1-bbaa73585acf  ...  MPE Control
2     a9b26a40-15da-11ee-bdf1-bbaa73585acf  ...
3     a8fc87c0-15da-11ee-bdf1-bbaa73585acf  ...  MPE Control
4     8e322990-15da-11ee-bdf1-bbaa73585acf  ...
...                                    ...  ...          ...
3624  907e1f40-6621-11ea-96e3-d5a4dab4ebf6  ...         C132
3625  53e59450-6621-11ea-96e3-d5a4dab4ebf6  ...         C132
3626  5d11b030-6618-11ea-96e3-d5a4dab4ebf6  ...         C132
3627  5bdf9270-6610-11ea-96e3-d5a4dab4ebf6  ...         C132
3628  dd607ef0-654c-11ea-8eb2-25a1cfd1163c  ...         C132

get_search_result

SeerSDK.get_search_result(analysis_id, analyte_type, rollup)

Load one of the files available via the “Download result files” button on the PAS UI.

Args: analysis_id (str): id of the analysis analyte_type (str): type of the data. Acceptable options are one of [‘protein’, ‘peptide’, ‘precursor’]. rollup (str): the desired file. Acceptable options are one of [‘np’, ‘panel’]. Returns: pd.DataFrame: the requested file as a pandas DataFrame

get_search_result_file_url

SeerSDK.get_search_result_file_url(analysis_id, filename)

Given an analysis id and a analysis result filename, this function returns the signed URL for the file.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis for which the data is to be fetched.	required
filename	str	Name of the file to be fetched.	required

Returns

Name	Type	Description
file_url	dict[str, str]	Dictionary containing the ‘url’ and ‘filename’ of the file.

get_spaces

SeerSDK.get_spaces()

Fetches a list of spaces for the authenticated user.

Returns

Name	Type	Description
spaces	list[dict]	List of space objects for the authenticated user.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> seer_sdk.get_spaces()
>>> [
        { "usergroup_name": ... },
        { "usergroup_name": ... },
        ...
    ]

get_user_tenant

SeerSDK.get_user_tenant(index=True)

Fetches the tenant metadata for the authenticated user.

Returns

Name	Type	Description
response	list[dict]	A list of tenant objects pertaining to the user.

get_volcano_plot_data

SeerSDK.get_volcano_plot_data(
    analysis_id,
    group_analysis_id=None,
    significance_threshold=0.05,
    fold_change_threshold=1,
    label_by='fold_change',
    cached=False,
    as_df=False,
)

Get volcano plot data for a given analysis ID.

Args: analysis_id (str): ID of the analysis. significance_threshold (float, optional): Cutoff value for the p-value to determine significance. Defaults to 0.05. fold_change_threshold (float, optional): Cutoff value for the fold change to determine significance. Defaults to 1. label_by (str, optional): Metric to sort result data. Defaults to “fold_change”. cached (bool, optional): Return a VolcanoPlotBuilder object for calculation reuse. Defaults to False. as_df (bool, optional): whether the result should be converted to a DataFrame. Defaults to False.

Raises: ServerError - could not fetch group analysis results. Returns: list[dict] | pd.DataFrame | VolcanoPlotBuilder: A list of dictionaries, a DataFrame, or a VolcanoPlotBuilder object containing the volcano plot data. Object contains the following columns: ‘logFD’, ‘negativeLog10P’, ‘dataIndex’, ‘rowID’, ‘gene’, ‘protein’, ‘group’, ‘significant’, ‘euclideanDistance’

group_analysis_results

SeerSDK.group_analysis_results(analysis_id, group_analysis_id=None)

Returns the group analysis data for the given analysis id, provided it exists.

If no group analysis id is provided, the function will return the most recent group analysis data for the given analysis id.

Parameters

Name	Type	Description	Default
analysis_id	str	The analysis id.	required
group_analysis_id	str	The group analysis id, defaulted to None.	None

Returns

Name	Type	Description
res	dict	A dictionary containing the group analysis object.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> seer_sdk = SeerSDK()
>>> seer_sdk.group_analysis_results("YOUR_ANALYSIS_ID_HERE")
>>> {
        "pre": {
            "protein": [],
            "peptide": [],
        },
        "post": {
            "protein": {},
            "protein_url": {
                "protein_processed_file_url": "",
                "protein_processed_long_form_file_url": "",
            },
            "peptide": {},
            "peptide_url": {
                "peptide_processed_file_url": "",
                "peptide_processed_long_form_file_url": "",
            },
        },
        "box_plot": []
    }

list_ms_data_files

SeerSDK.list_ms_data_files(folder='', space=None)

Lists all the MS data files in the given folder as long as the folder path passed in the params is valid.

Parameters

Name	Type	Description	Default
folder	str	Folder path to list the files from. Defaults to an empty string and displays all files for the user.	''
space	str	ID of the user group to which the files belong, defaulted to None.	None

Returns

Name	Type	Description
	list[str]	Contains the list of files in the folder.

Examples

>>> from seer_pas_sdk import SeerSDK
>>> sdk = SeerSDK()
>>> folder_path = "test-may-2/"
>>> sdk.list_ms_data_files(folder_path)
>>> [
    "test-may-2/EXP20028/EXP20028_2020ms0096X10_A.raw",
    "test-may-2/agilent/05_C2_19ug-r001.d.zip",
    "test-may-2/agilent/08_BC_24ug-r001.d.zip",
    "test-may-2/d.zip/EXP22023_2022ms0143bX10_A_GA2_1_6681.d/EXP22023_2022ms0143bX10_A_GA2_1_6681.d.zip",
    "test-may-2/DIA/EXP20002_2020ms0142X10_A.wiff",
    "test-may-2/DIA/EXP20002_2020ms0142X10_A.wiff.scan",
    "test-may-2/DIA/EXP20002_2020ms0142X17_A.wiff",
    "test-may-2/DIA/EXP20002_2020ms0142X17_A.wiff.scan",
    "test-may-2/DIA/EXP20002_2020ms0142X18_A.wiff",
    "test-may-2/DIA/EXP20002_2020ms0142X18_A.wiff.scan"
]

list_search_result_files

SeerSDK.list_search_result_files(analysis_id, folder=None, recursive=False)

Given an analysis id, this function returns a list of files associated with the analysis.

Parameters

Name	Type	Description	Default
analysis_id	str	ID of the analysis for which the data is to be fetched.	required
folder	str	Root folder key to list search result files from, defaulted to None.	None
recursive	bool	Whether to list files recursively from subfolders, defaulted to False.	False

Returns

Name	Type	Description
files	list[str]	List of files associated with the analysis.

list_tenants

SeerSDK.list_tenants(reverse=False)

Lists the institution names and the tenant ids for the authenticated user.

Parameters

Name	Type	Description	Default
reverse		Boolean denoting whether the user wants the result dictionary indexed by tenant id (True) or institution name (False).	False

Returns

Name	Type	Description
tenants	dict[str, str]	A dictionary containing the institution names and tenant ids for the authenticated user.

switch_tenant

SeerSDK.switch_tenant(identifier)

Switches the tenant for the authenticated user.

Parameters

Name	Type	Description	Default
identifier	str	Tenant ID or organization name to switch to.	required

Returns

Name	Type	Description
tenant_id	str	Returns the value of the active tenant id after the operation.