Source code for besca.st._FAIR_export

# this contains wrapper functions to export data into the standard format for the standard pipeline

# import other functions
from besca.export._export import (
    X_to_mtx,
    raw_to_mtx,
    clustering,
    write_labeling_to_files,
    analysis_metadata,
    ranked_genes,
    labeling_info,
)
from besca.Import._read import read_mtx
from besca import _logging as logs
from os.path import join
from os import makedirs
import os
from time import time
import logging
from besca.pp._filtering import filter


def export_cp10k(adata, basepath):
    """Export raw cp10k to FAIR format for loading into database

    wrapper function for X_to_mtx with correct folder structure for loading into database.

    parameters
    ----------
    adata: `ÀnnData`
        AnnData object that is to be exported
    basepath: `str`
        root path to the Analysis folder (i.e. ../analyzed/<ANALYSIS_NAME>)

    returns
    -------
    None
        writes to file

    """

    # call wrapper function
    X_to_mtx(
        adata=adata,
        outpath=join(basepath, "normalized_counts", "cp10k"),
        write_metadata=True,
        geneannotation="SYMBOL",
        additional_geneannotation="ENSEMBL",
    )


def export_norm_citeseq(adata, basepath):
    """Export corrected CiteSeq data to FAIR format for loading into database

    wrapper function for X_to_mtx with correct folder structure for loading into database.

    parameters
    ----------
    adata: `AnnData`
        AnnData object that is to be exported. Needs to be CiteSeq data.
    basepath: `str`
        root path to the Analysis folder (i.e. ../analyzed/<ANALYSIS_NAME>)

    returns
    -------
    None
        writes to file

    """

    # call wrapper function
    X_to_mtx(
        adata=adata,
        outpath=join(basepath, "normalized_counts"),
        write_metadata=True,
        geneannotation="SYMBOL",
        additional_geneannotation="ENSEMBL",
    )


def export_regressedOut(adata, basepath):
    """Export regressedOut to FAIR format for loading into database

    wrapper function for X_to_mtx with correct folder structure for loading into database.

    parameters
    ----------
    adata: `ÀnnData`
        AnnData object that is to be exported
    basepath: `str`
        root path to the Analysis folder (i.e. ../analyzed/<ANALYSIS_NAME>)

    returns
    -------
    None
        writes to file

    """
    X_to_mtx(
        adata,
        outpath=join(basepath, "normalized_counts", "regressedOut"),
        geneannotation="SYMBOL",
        write_metadata=True,
        additional_geneannotation="ENSEMBL",
    )


def export_clustering(adata, basepath, method):
    """Export cluster to cell mapping to FAIR format for loading into database

    wrapper function for louvain and labeling_info with correct folder structure/names
    for loading into the database.

    parameters
    ----------
    adata: `ÀnnData`
        AnnData object that is to be exported
    basepath: `str`
        root path to the Analysis folder (i.e. ../analyzed/<ANALYSIS_NAME>)
    method: `str`
        method of clustering used previously, should be leiden or louvain

    returns
    -------
    None
        writes to file
    """

    clustering(adata, outpath=join(basepath, "labelings", method), method=method)
    labeling_info(
        outpath=join(basepath, "labelings", method),
        description=method + " clustering",
        method=method,
    )


def export_metadata(adata, basepath, n_pcs=3, umap=True, tsne=False):
    """Export metadata in FAIR format for loading into database

    wrapper function for analysis_metadata with correct folder structure/names
    for loading into the database.

    parameters
    ----------
    adata: `ÀnnData`
        AnnData object that is to be exported
    basepath: `str`
        root path to the Analysis folder (i.e. ../analyzed/<ANALYSIS_NAME>)
    n_pcs: `int` | default = 3
        number of PCA components to export
    umap: `bool` | default = True
        boolian indicator if umap coordinates should be exported
    tsne: `bool` | default = False
        boolian indicator if tSNE coordinates should be exported

    returns
    -------
    None
        writes to file

    """

    analysis_metadata(adata, outpath=join(basepath), n_pcs=n_pcs, umap=umap, tsne=tsne)


def export_rank(adata, basepath, type="wilcox", labeling_name="louvain"):
    """Export ranked genes to FAIR format for loading into database

    wrapper function for ranked_genes with correct folder structure/names
    for loading into the database.

    parameters
    ----------
    adata: `ÀnnData`
        AnnData object that is to be exported
    basepath: `str`
        root path to the Analysis folder (i.e. ../analyzed/<ANALYSIS_NAME>)
    type: `str` | default = 'wilcox'
        indicator of the statistical method employed, can be one of: 'wilcox' or 't-test overest var'  or 't-test'
    labelingname: `str` | default = `louvain`
        labeling that will be exported

    returns
    -------
    None
        writes to file

    """
    # export rank files
    ranked_genes(
        adata=adata, outpath=join(basepath, "labelings", labeling_name), type=type
    )


def export_celltype(adata, basepath):
    """Export celltype annotation to cell mapping in FAIR format for loading into database

    wrapper function for labeling and labeling_info with correct folder structure/names
    for loading into the database.

    parameters
    ----------
    adata: `ÀnnData`
        AnnData object that is to be exported
    basepath: `str`
        root path to the Analysis folder (i.e. ../analyzed/<ANALYSIS_NAME>)

    returns
    -------
    None
        writes to file

    """

    # export celltypes
    write_labeling_to_files(
        adata=adata, outpath=join(basepath, "labelings", "dblabel"), column="dblabel"
    )

    labeling_info(
        outpath=join(basepath, "labelings", "dblabel"),
        method="celltype annotation based on marker expression",
        annotated_version_of="leiden",
        expert=True,
        default=False,
        public=False,
        reference=True,
        description="manual celltype annotation based on the expression of marker genes",
    )