napistu 0.2.5.dev7__py3-none-any.whl → 0.3.1.dev1__py3-none-any.whl

napistu/rpy2/netcontextr.py

@@ -1,467 +0,0 @@
-"""Module containing functions to interoperate with rcpr's netcontextr functions"""
-
-from __future__ import annotations
-
-import logging
-import os
-from tempfile import NamedTemporaryFile
-from typing import Any
-from typing import Callable
-from typing import Iterable
-
-import pandas as pd
-from napistu import sbml_dfs_core
-from napistu import utils
-from napistu.rpy2 import has_rpy2
-from napistu.rpy2 import warn_if_no_rpy2
-
-from napistu.rpy2.constants import COL_GENE
-from napistu.rpy2.constants import COL_PROTEIN_1
-from napistu.rpy2.constants import COL_PROTEIN_2
-from napistu.rpy2.constants import FIELD_INTERACTIONS
-from napistu.rpy2.constants import FIELD_GENES
-from napistu.rpy2.constants import FIELD_REACTIONS
-from napistu.rpy2.constants import COL_ROLE
-from napistu.rpy2.constants import COL_REACTION_ID
-from napistu.rpy2.constants import COL_STOICHIOMETRY
-from napistu.rpy2.constants import NETCONTEXTR_ONTOLOGY
-from napistu.rpy2.constants import NETCONTEXTR_SBO_MAP
-
-if has_rpy2:
-    from napistu.rpy2.callr import pandas_to_r_dataframe
-    from rpy2.robjects import ListVector
-    import rpy2.robjects as robjs
-
-logger = logging.getLogger(__name__)
-
-
-@warn_if_no_rpy2
-def _none2null(none_obj):
-    return robjs.r("NULL")
-
-
-@warn_if_no_rpy2
-def sbml_dfs_to_rcpr_string_graph(
-    sbml_dfs: sbml_dfs_core.SBML_dfs,
-    reaction_data: str = "string",
-    identifier_ontology: str = "ensembl_gene",
-    rescale_data: Callable[[pd.DataFrame], pd.DataFrame] | None = lambda x: x / 1000,
-) -> ListVector:
-    """Converts an sbml_dfs to a rcpr string graph
-
-    This utility converts the sbml_dfs to the format returned
-    by `rcpr::createStringGraph`.
-
-    Args:
-        sbml_dfs (SBML_dfs): the sbml_dfs from string.
-            It is assumed that this sbml_dfs has only reactions with exactly
-            two reactands and a 1:1 mapping between s_id and sc_id.
-        reaction_data (str, optional): The reaction data that contains
-            the string scores. Defaults to 'string'.
-        identifier_ontology (str, optional): The ontology to use for the
-            protein identifiers. Defaults to `ensembl_gene` (default in rcpr)
-        rescale_data (Callable[pd.DataFrame], optional): A function to rescale
-            the data. Defaults to lambda x: x/1000 (default in rcpr)
-
-    Returns:
-        This is a list of dataframes almost the same as `rcpr::createStringGraph`:
-        - `genes`: a dataframe with column `gene`
-            and the extra column `s_id`, `sc_id`
-        - `interactions`: a dataframe with columns `protein1`, `protein2` and
-            the scores from string
-            and the extra column `r_id`
-
-        The extra columns `s_id` and `r_id` are used to map the genes and reactions
-        to the sbml_dfs. This is useful for mapping back rcpr results to the
-        sbml_dfs.
-    """
-
-    dat_gene = (
-        sbml_dfs.species["s_Identifiers"]
-        # Get the identifiers for the given ontology
-        .map(lambda ids: ids.hoist(identifier_ontology))
-        .rename(COL_GENE)
-        .to_frame()
-        # Merge with compartmentalized species to get the sc_id
-        .merge(
-            sbml_dfs.compartmentalized_species[["s_id"]].reset_index(drop=False),
-            left_index=True,
-            right_on="s_id",
-        )[[COL_GENE, "sc_id", "s_id"]]
-    )
-
-    # Perform validations
-    if not dat_gene["s_id"].is_unique:
-        raise ValueError("dat_gene['s_id'] must be unique")
-    if not dat_gene["sc_id"].is_unique:
-        raise ValueError("dat_gene['sc_id'] must be unique")
-    if not dat_gene[COL_GENE].is_unique:
-        raise ValueError("dat_gene[COL_GENE] must be unique")
-    if dat_gene[COL_GENE].hasnans:
-        raise ValueError("dat_gene[COL_GENE] must not have NaNs")
-
-    # Reshape into the correct format
-    dat_reactions = dat_gene[["sc_id", COL_GENE]].merge(
-        sbml_dfs.reaction_species[["r_id", "sc_id"]], on="sc_id"
-    )[[COL_GENE, "r_id"]]
-    # assert that this has the correct shape, ie 2x the shape of the number
-    # of reactions
-    if dat_reactions.shape[0] != 2 * sbml_dfs.reactions.shape[0]:
-        raise ValueError("There should be exactly 2 reactants per reaction")
-
-    # This is the fastest way I found to reshape this into the
-    # Edgelist format
-    dat_reactions["flag"] = dat_reactions["r_id"].duplicated()
-    dat_interactions = dat_reactions.pivot(
-        index="r_id", columns="flag", values=COL_GENE
-    )
-    dat_interactions.columns = pd.Index([COL_PROTEIN_1, COL_PROTEIN_2], dtype=object)
-    if rescale_data is not None:
-        reaction_df = rescale_data(sbml_dfs.reactions_data[reaction_data])
-    else:
-        reaction_df = sbml_dfs.reactions_data[reaction_data]
-
-    dat_interactions = dat_interactions.join(reaction_df).reset_index(drop=False)
-
-    genes = pandas_to_r_dataframe(dat_gene)
-    interactions = pandas_to_r_dataframe(dat_interactions)
-
-    out = ListVector({FIELD_GENES: genes, FIELD_INTERACTIONS: interactions})
-    return out
-
-
-@warn_if_no_rpy2
-def load_and_clean_hpa_data(
-    rcpr,
-    uri_hpa: str,
-):
-    """Load and cleans HPA data using rcpr
-
-    Args:
-        rcpr (): The rpy2 rcpr object
-        uri_hpa (str): The uri of the HPA data
-
-    Returns:
-        rpy2 object: The cleaned HPA data
-    """
-
-    with NamedTemporaryFile() as f:
-        # R cannot work with gcs uris
-        # thus download the file to a temporary
-        # location incase it is a gcs uri
-        if os.path.exists(uri_hpa):
-            # if the file is already a local
-            # file, just use it
-            path_hpa = uri_hpa
-        else:
-            path_hpa = f.name
-            utils.copy_uri(uri_hpa, path_hpa)
-
-        hpa_localization_data = rcpr.load_and_clean_hpa_data(path_hpa)
-    return hpa_localization_data
-
-
-@warn_if_no_rpy2
-def load_and_clean_gtex_data(rcpr_rpy2, uri_gtex: str, by_tissue_zfpkm: bool = False):
-    """Load and cleans GTEx data using rcpr
-
-    Args:
-        rcpr_rpy2 (): The rpy2 rcpr object
-        uri_gtex (str): The uri of the GTEx data
-        by_tissue_zfpkm (bool, optional): Whether to return the data normalized
-          by tissue using zfpkm. Defaults to False.
-    Returns:
-        rpy2 object: The cleaned GTEx data
-    """
-    with NamedTemporaryFile() as f:
-        # R cannot work with gcs uris
-        # thus download the file to a temporary
-        # location incase it is a gcs uri
-        if os.path.exists(uri_gtex):
-            # if the file is already a local
-            # file, just use it
-            path_gtex = uri_gtex
-        else:
-            path_gtex = f.name
-            utils.copy_uri(uri_gtex, path_gtex)
-
-        gtex_tissue_data = rcpr_rpy2.load_and_clean_gtex_data(path_gtex)
-
-    if by_tissue_zfpkm:
-        gtex_tissue_data = rcpr_rpy2.gene_expression_by_tissue(gtex_tissue_data)
-    return gtex_tissue_data
-
-
-def annotate_genes(
-    rcpr, rcpr_graph: ListVector, data, field_name: str, **kwargs
-) -> ListVector:
-    """Annotates the genes in the graph with the given gene data
-
-    See the rcpr documentation about the exact format
-    required.
-
-    Args:
-        rcpr (): The rpy2 rcpr object
-        rcpr_graph (ListVector): The graph to annotate
-        data (complicated): "
-        field_name (str): The name of the column in the gene data to annotate with
-
-    Returns:
-        ListVector: The annotated graph
-    """
-    # Annotate the genes
-    rcpr_graph_annot = rcpr.annotate_genes(rcpr_graph, data, field_name, **kwargs)
-    return rcpr_graph_annot
-
-
-def trim_network_by_gene_attribute(
-    rcpr,
-    rcpr_graph: ListVector,
-    field_name: str,
-    field_value: Any = None,
-    **kwargs,
-) -> ListVector:
-    """Trims the network by a gene attribute
-
-    See the R function `rcpr::trim_network_by_gene_attribute` for
-    more details.
-
-    Args:
-        rcpr (): The rpy2 rcpr object
-        rcpr_graph (ListVector): The graph to trim
-        field_name (str): The name of the column in the gene data to trim by
-        field_value (Any): One or more values to trim by
-
-    Returns:
-        ListVector: The trimmed graph
-    """
-    if field_value is None:
-        field_value = robjs.r("NaN")
-    rcpr_graph_trimmed = rcpr.trim_network_by_gene_attribute(
-        rcpr_graph, field_name=field_name, field_value=field_value, **kwargs
-    )
-    return rcpr_graph_trimmed
-
-
-def apply_context_to_sbml_dfs(
-    sbml_dfs: sbml_dfs_core.SBML_dfs,
-    rcpr_graph: ListVector,
-    inplace=True,
-    remove_species=False,
-) -> sbml_dfs_core.SBML_dfs:
-    """Applies the context to the SBML dfs
-
-    This is currently an in-place modification of
-    the sbml_dfs object.
-
-    Args:
-        sbml_dfs (SbmlDfs): The SBML dfs to apply the context to
-        rcpr_graph (ListVector): The graph to apply the context from
-        inplace (bool, optional): Whether to modify the sbml_dfs in-place
-            when applying the context. Defaults to True. "False" not yet implemented.
-        remove_species (bool, optional): Whether to remove
-            (compartmentalized) species that are no longer in the reactions.
-            Defaults to False.
-
-    Returns:
-        SbmlDfs: The SBML dfs with the context applied
-    """
-    if not inplace:
-        raise NotImplementedError("Only inplace is currently supported")
-
-    # r_ids after trimming
-    r_ids_new = set(rcpr_graph.rx("interactions")[0].rx("r_id")[0])
-
-    # find original r_ids
-    r_ids_old = set(sbml_dfs.reactions.index.tolist())
-
-    # find the r_ids that are in the original but not in the new
-    r_ids_to_remove = r_ids_old - r_ids_new
-
-    # assert that no new r_ids were added
-    if len(diff_ids := r_ids_new - r_ids_old) != 0:
-        raise ValueError(
-            f"New reactions present in rcpr, not present in smbl_dfs: {', '.join(diff_ids)}"
-        )
-
-    sbml_dfs.remove_reactions(r_ids_to_remove, remove_species=remove_species)
-
-    return sbml_dfs
-
-
-def sbml_dfs_to_rcpr_reactions(
-    sbml_dfs: sbml_dfs_core.SBML_dfs,
-    identifier_ontology: str = NETCONTEXTR_ONTOLOGY,
-) -> ListVector:
-    """Converts an sbml_dfs to a rcpr reaction graph
-
-    This utility converts the sbml_dfs to the format validated by
-    by `rcpr::validate_netcontextr_reactions`.
-
-    It converts the smbl_dfs into a reaction graph by:
-    - Building the `reactions` dataframe:
-        - Using the `species` identifiers to map `reaction_species`
-            to `genes` using the `identifier_ontology`.
-            Note that one species may be split into multiple `genes`
-            and multiple species may be combined into a single `gene`.
-        - Converting `sbo_terms` to roles.
-        - renaming `r_id` to `reaction_id`
-    - Building `genes` dataframe by taking all unique `genes` from the `reactions`
-
-    Args:
-        sbml_dfs (SBML_dfs): an sbml_dfs.
-        identifier_ontology (str, optional): The ontology to use for the
-             identifiers. Defaults to `ensembl_gene` (default in rcpr)
-
-    Returns:
-        This is a list of dataframes that validate with validate_netcontextr_reactions:
-        - `genes`: a dataframe with column `gene`
-        - `reactions`: a dataframe with columns "gene", "reaction_id", "role", "rsc_id"
-            representing the reaction data split up into individual reactions.
-    """
-
-    # Get the reactions
-    dat_reactions = _get_reactions(sbml_dfs, identifier_ontology)
-    # Get the genes
-    dat_gene = dat_reactions[[COL_GENE]].drop_duplicates()
-    # Note that no 1:1 mapping between genes and species can be made
-    # as multiple species could have the same gene annotation
-    # and also even one species could have multiple gene identifiers
-    genes = pandas_to_r_dataframe(dat_gene)
-    reactions = pandas_to_r_dataframe(dat_reactions)
-
-    out = ListVector({FIELD_GENES: genes, FIELD_REACTIONS: reactions})
-    return out
-
-
-def trim_reactions_by_gene_attribute(
-    rcpr,
-    rcpr_reactions: ListVector,
-    field_name: str,
-    field_value: Any = None,
-    **kwargs,
-) -> ListVector:
-    """Trims rcpr reactions by a gene attribute
-
-    See the R function `rcpr::trim_reactions_by_gene_attribute` for
-    more details.
-
-    Args:
-        rcpr (): The rpy2 rcpr object
-        rcpr_reactions (ListVector): The graph to trim
-        field_name (str): The name of the column in the gene data to trim by
-        field_value (Any): One or more values to trim by
-
-    Returns:
-        ListVector: The trimmed graph
-    """
-    if field_value is None:
-        field_value = robjs.r("NaN")
-    rcpr_reactions_trimmed = rcpr.trim_reactions_by_gene_attribute(
-        rcpr_reactions, field_name=field_name, field_value=field_value, **kwargs
-    )
-    return rcpr_reactions_trimmed
-
-
-def apply_reactions_context_to_sbml_dfs(
-    sbml_dfs: sbml_dfs_core.SBML_dfs,
-    rcpr_reactions: ListVector,
-    considered_reactions: Iterable[str] | None = None,
-    inplace=True,
-    remove_species=False,
-) -> sbml_dfs_core.SBML_dfs:
-    """Applies the context to the SBML dfs
-
-    This is currently an in-place modification of
-    the sbml_dfs object.
-
-    Args:
-        sbml_dfs (sbml_dfs_core.SBML_dfs): The SBML dfs to apply the context to
-        rcpr_reactions (ListVector): The contextualized
-        considered_reactions (Iterable[str], optional): The reactions that were
-            considered for contextualisation. If None, all reactions that are
-            in the sbml_dfs are considered and filtered out if they are not part of
-            the rcpr_reactions. If provided, only reactions considered and not part
-            of the rcpr_reactions are removed. Defaults to None.
-        inplace (bool, optional): Whether to apply the context inplace.
-            Only True currently implemented.
-        remove_species (bool, optional): Whether to remove
-            (compartmentalized) species that are no longer in the reactions.
-            Defaults to False.
-
-    Returns:
-        SbmlDfs: The SBML dfs with the context applied
-    """
-    if not inplace:
-        raise NotImplementedError("Only inplace is currently supported")
-
-    # r_ids after trimming
-    r_ids_new = _get_rids_from_rcpr_reactions(rcpr_reactions)
-
-    # find original r_ids
-    if considered_reactions is None:
-        r_ids_old = set(sbml_dfs.reactions.index.tolist())
-    else:
-        r_ids_old = set(considered_reactions)
-
-    # find the r_ids that are in the original but not in the new
-    r_ids_to_remove = r_ids_old - r_ids_new
-
-    # assert that no new r_ids were added
-    if len(diff_ids := r_ids_new - r_ids_old) != 0:
-        raise ValueError(
-            "New reactions present in rcpr, not present in the considered "
-            f"reactions: {', '.join(diff_ids)}"
-        )
-
-    sbml_dfs.remove_reactions(r_ids_to_remove, remove_species=remove_species)
-
-    return sbml_dfs
-
-
-def _get_rids_from_rcpr_reactions(rcpr_reactions: ListVector) -> set[str]:
-    """Gets the r_ids from the rcpr reactions"""
-    return set(rcpr_reactions.rx(FIELD_REACTIONS)[0].rx(COL_REACTION_ID)[0])
-
-
-def _get_reactions(
-    sbml_dfs: sbml_dfs_core.SBML_dfs, identifier_ontology: str = NETCONTEXTR_ONTOLOGY
-) -> pd.DataFrame:
-    """Gets the reactions from the sbml_dfs"""
-    dat_reaction = (
-        sbml_dfs.species["s_Identifiers"]
-        # Get the identifiers for the given ontology
-        .map(lambda ids: ids.hoist(identifier_ontology, squeeze=False))
-        .map(lambda x: x if len(x) > 0 else None)
-        .dropna()
-        .rename(COL_GENE)
-        .to_frame()
-        .explode(COL_GENE)
-        # Merge with compartmentalized species to get the sc_id
-        .merge(
-            sbml_dfs.compartmentalized_species[["s_id"]].reset_index(drop=False),
-            left_index=True,
-            right_on="s_id",
-        )[[COL_GENE, "sc_id"]]
-        .merge(
-            sbml_dfs.reaction_species[
-                ["r_id", "sc_id", "sbo_term", "stoichiometry"]
-            ].reset_index(drop=False),
-            on="sc_id",
-        )
-        .assign(**{COL_ROLE: lambda x: x["sbo_term"].map(NETCONTEXTR_SBO_MAP)})
-        .rename({"r_id": COL_REACTION_ID, "stoichiometry": COL_STOICHIOMETRY}, axis=1)
-    )
-    fil = dat_reaction[COL_ROLE].isna()
-    if fil.sum() > 0:
-        missing_sbo_terms = dat_reaction.loc[fil, "sbo_term"].unique()
-        logger.warning(
-            f"Found {fil.sum()} reactions had an sbo term that was not"
-            "mappable to a rcpr role. These are ignored. "
-            f"The sbo terms are: {', '.join(missing_sbo_terms)}"
-        )
-
-        dat_reaction = dat_reaction.loc[~fil, :]
-    return dat_reaction[
-        [COL_ROLE, COL_GENE, COL_REACTION_ID, COL_STOICHIOMETRY, "rsc_id"]
-    ]

napistu-0.2.5.dev7.dist-info/RECORD

@@ -1,98 +0,0 @@
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-napistu/ingestion/sbml.py,sha256=gK6_jHgo6oaiG16WlrbBSvxq_0VzFR4a5fG9IQrp5bU,24153
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