gsMap 1.71__py3-none-any.whl → 1.71.1__py3-none-any.whl

gsMap/utils/make_annotations.py

@@ -1,518 +1,518 @@
-import argparse
-import logging
-import os
-import pprint
-import time
-from pathlib import Path
-
-
-import numpy as np
-import pandas as pd
-import pyranges as pr
-from progress.bar import IncrementalBar
-
-from gsMap.utils.generate_r2_matrix import PlinkBEDFileWithR2Cache, getBlockLefts, ID_List_Factory
-
-
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.DEBUG)
-handler = logging.StreamHandler()
-handler.setFormatter(logging.Formatter(
-    '[{asctime}] {levelname:8s} {filename} {message}', style='{'))
-logger.addHandler(handler)
-from dataclasses import dataclass, field
-from typing import Optional
-try:
-    import cupy as cp
-    pool = cp.cuda.MemoryPool(cp.cuda.malloc_async)
-    cp.cuda.set_allocator(pool.malloc)
-except ImportError:
-    logger.warning('Cupy not found, will not use GPU to compute LD score')
-    cp = None
-@dataclass
-class MakeAnnotationConfig:
-    input_feather_file: str
-    output_dir: str
-    sample_name: str
-    gtf_file: Optional[str] = None
-    bfile_root: Optional[str] = None
-    baseline_annotation: Optional[str] = None
-    keep_snp_root: Optional[str] = None
-    chr: Optional[int] = None
-    window_size: int = 50000
-    cells_per_chunk: int = 500
-    ld_wind: float = 1.0
-    ld_wind_unit: str = field(default='CM', metadata={'choices': ['CM', 'BP', 'SNP']})
-    r2_cache_dir: Optional[str] = None
-    use_gpu: bool = False
-    snps_per_chunk: int = 50_000
-
-    def __post_init__(self):
-        if self.ld_wind_unit not in self.__dataclass_fields__['ld_wind_unit'].metadata['choices']:
-            raise ValueError(f"Invalid ld_wind_unit: {self.ld_wind_unit}. Choose from 'CM', 'BP', or 'SNP'.")
-
-
-class Snp_Annotator:
-    """
-    1. Annotate SNPs based on score of genes.
-    2. Add baseline annotations.
-    """
-
-    def __init__(self, mk_score_file, gtf_file, bfile_root, annot_root, annot_name, chr=None, base_root=None,
-                 window_size=50000, const_max_size=100):
-        #
-        # marker score
-        self.mk_score_file = mk_score_file
-        self.mk_score = self.load_marker_score()
-        #
-        # chunk cells
-        # self.const_max_size = const_max_size
-        self.n_cells = len(self.mk_score.columns)
-        self.max_chunk = const_max_size
-        # self.max_chunk = floor(self.n_cells / self.const_max_size)
-        #
-        # gtf data
-        self.gtf_file = gtf_file
-        self.window_size = window_size
-        self.gtf_pr = self.load_gtf(mk_score=self.mk_score)
-        #
-        self.bfile_root = bfile_root
-        self.annot_root = annot_root
-        self.base_root = base_root
-        self.chr = chr
-
-        self.data_name = annot_name
-
-    #
-    def load_marker_score(self):
-        """
-        Load marker scores of each cell.
-        """
-        mk_score = pd.read_feather(self.mk_score_file).set_index('HUMAN_GENE_SYM').rename_axis('gene_name')
-        mk_score.insert(0, 'all_gene', 1)
-        return mk_score
-
-    #
-    def load_gtf(self, mk_score):
-        """
-        Load the gene annotation file (gtf).
-        """
-        print("Loading gtf data")
-        #
-        # Load GTF file
-        gtf = pr.read_gtf(self.gtf_file)
-        gtf = gtf.df
-        #
-        # Select the common genes
-        gtf = gtf[gtf['Feature'] == 'gene']
-        common_gene = np.intersect1d(mk_score.index, gtf.gene_name)
-        #
-        gtf = gtf[gtf.gene_name.isin(common_gene)]
-        mk_score = mk_score[mk_score.index.isin(common_gene)]
-        #
-        # Remove duplicated lines
-        gtf = gtf.drop_duplicates(subset='gene_name', keep="first")
-        #
-        # Process the GTF (open 100-KB window: Tss - Ted)
-        gtf_bed = gtf[['Chromosome', 'Start', 'End', 'gene_name', 'Strand']].copy()
-        gtf_bed.loc[:, 'TSS'] = gtf_bed['Start']
-        gtf_bed.loc[:, 'TED'] = gtf_bed['End']
-
-        gtf_bed.loc[:, 'Start'] = gtf_bed['TSS'] - self.window_size
-        gtf_bed.loc[:, 'End'] = gtf_bed['TED'] + self.window_size
-        gtf_bed.loc[gtf_bed['Start'] < 0, 'Start'] = 0
-        #
-        # Correct the negative strand
-        tss_neg = gtf_bed.loc[gtf_bed['Strand'] == '-', 'TSS']
-        ted_neg = gtf_bed.loc[gtf_bed['Strand'] == '-', 'TED']
-        gtf_bed.loc[gtf_bed['Strand'] == '-', 'TSS'] = ted_neg
-        gtf_bed.loc[gtf_bed['Strand'] == '-', 'TED'] = tss_neg
-        gtf_bed = gtf_bed.drop('Strand', axis=1)
-        #
-        # Transform the GTF to PyRanges
-        gtf_pr = pr.PyRanges(gtf_bed)
-        return gtf_pr
-
-    #
-    def load_baseline(self, chr):
-        """
-        Load baseline annotations.
-        """
-        baseline = pd.read_csv(f'{self.base_root}.{chr}.annot.gz', sep='\t')
-        baseline.drop(['CHR', 'BP', 'CM'], axis=1, inplace=True)
-        return baseline
-
-    # -
-    def Load_bim(self, chr):
-        """
-        Load bim files.
-        """
-        bim_file = f'{self.bfile_root}.{chr}.bim'
-        bim = pd.read_csv(bim_file, sep='\t', header=None)
-        bim.columns = ["CHR", "SNP", "CM", "BP", "A1", "A2"]
-        #
-        # Transform bim to PyRanges
-        bim_pr = bim.copy()
-        bim_pr.columns = ["Chromosome", "SNP", "CM", "Start", "A1", "A2"]
-        bim_pr['End'] = bim_pr['Start']
-        bim_pr = pr.PyRanges(bim_pr)
-        bim_pr.Chromosome = f'chr{chr}'
-        return bim_pr, bim
-
-    # -
-    def Overlaps_gtf_bim(self, bim_pr):
-        """
-        Find overlaps between gtf and bim file.
-        """
-        # Select the overlapped regions (SNPs in gene windows)
-        overlaps = self.gtf_pr.join(bim_pr)
-        overlaps = overlaps.df
-        overlaps['Distance'] = np.abs(overlaps['Start_b'] - overlaps['TSS'])
-        overlaps_small = overlaps.copy()
-        overlaps_small = overlaps_small.loc[overlaps_small.groupby('SNP').Distance.idxmin()]
-        return overlaps_small
-
-    # -
-    def map_baseline(self, snp_score, baseline, chr):
-        """
-        Generate the baseline annotations for SNPs.
-        """
-
-        header = snp_score.columns[0:6].to_list()
-
-        if baseline is None:
-            print(f'Baseline annotations of chr{chr} are not provided, using uniform annotations for genes and SNPs')
-            baseline_score = snp_score[header + ['all_gene']].copy()
-            baseline_score.loc[:, 'base'] = 1
-
-        else:
-            print(f'Mapping baseline annotations of chr{chr}')
-            snp_score_baseline = pd.merge(snp_score, baseline, how='left', on='SNP').fillna(0).copy()
-
-            baseline_score = snp_score_baseline[header + ['all_gene'] + baseline.columns.to_list()]
-            baseline_score = baseline_score.loc[:, ~baseline_score.columns.duplicated()].copy()
-
-        # Create the folder (for baseline annotation)
-        file_base_root = f'{self.annot_root}/baseline'
-        if not os.path.exists(file_base_root):
-            os.makedirs(file_base_root, mode=0o777, exist_ok=True)
-
-            # Save baseline annotations (in parquet format)
-        file_base = f'{file_base_root}/baseline.{chr}.feather'
-        baseline_score.to_feather(file_base)
-
-        return 0
-
-    # -
-    def annotate_chr(self, chr):
-        """
-        Annotate SNPs of each chr.
-        """
-        # Load the baseline file
-        baseline = None
-        if self.base_root is not None:
-            baseline = self.load_baseline(chr)
-
-        # Load the bim file
-        bim_pr, bim = self.Load_bim(chr)
-
-        # Find overlapping
-        overlaps_small = self.Overlaps_gtf_bim(bim_pr)
-
-        # Do annotations
-        all_chunks = int(np.ceil(self.n_cells / self.max_chunk))
-        bar = IncrementalBar(f'Mapping the gene marker scores to SNPs in chr{chr}', max=all_chunks)
-        bar.check_tty = False
-
-        # Preprocess bim outside the loop as it doesn't change
-        anno_template = bim[["CHR", "BP", "SNP", "CM"]]
-
-        for chunk_index, left in enumerate(range(0, self.n_cells, self.max_chunk), start=1):
-            right = min(left + self.max_chunk, self.n_cells)
-            mk_score_current = self.mk_score.iloc[:, left:right]
-
-            # Process marker scores for SNPs
-            anno = anno_template.copy()
-            merged_data = overlaps_small[['SNP', 'gene_name', 'TSS']].merge(mk_score_current, on='gene_name',
-                                                                            how='left')
-            snp_score = pd.merge(anno, merged_data, how='left', on='SNP').fillna(0)
-            snp_score = snp_score.rename(columns={'gene_name': 'Gene'})
-            snp_score.loc[snp_score.Gene == 0, 'Gene'] = 'None'
-
-            # Process baseline annotations for the first chunk
-            if chunk_index == 1:
-                self.map_baseline(snp_score, baseline, chr)
-                snp_score = snp_score.drop('all_gene', axis=1)
-
-            # Create the folder and save SNP annotations
-            file_root = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}'
-            os.makedirs(file_root, mode=0o777, exist_ok=True)
-            file_anno = f'{file_root}/{self.data_name}.{chr}.feather'
-            snp_score.to_feather(file_anno)
-
-            bar.next()
-
-        bar.finish()
-
-        return all_chunks
-
-    #
-    def annotate(self):
-        """
-        Perform SNP annotations for each chromosome.
-        """
-        if self.chr == None:
-            for chr in range(1, 23):
-                const_max_size = self.annotate_chr(chr=chr)
-        else:
-            const_max_size = self.annotate_chr(chr=self.chr)
-
-        return const_max_size
-
-
-class LDscore_Generator:
-    def __init__(self, make_annotation_config: MakeAnnotationConfig, const_max_size):
-        self.bfile_root = make_annotation_config.bfile_root
-        self.annot_root = Path(make_annotation_config.output_dir)
-        self.const_max_size = const_max_size
-        self.data_name = make_annotation_config.sample_name
-        self.chr = make_annotation_config.chr
-        self.ld_wind = make_annotation_config.ld_wind
-        self.ld_wind_unit = make_annotation_config.ld_wind_unit
-        self.keep_snp = make_annotation_config.keep_snp_root
-        self.r2_cache_dir = make_annotation_config.r2_cache_dir
-        self.use_gpu = make_annotation_config.use_gpu
-        self.config = make_annotation_config
-        self.generate_r2_cache = False
-
-        # Set the r2 cache
-        if self.r2_cache_dir is None:
-            logger.info('No r2 cache directory specified, will not use r2 cache')
-            self.chr_r2_cache_dir = None
-        else:
-            assert self.chr is not None, 'Must specify chr when using r2 cache'
-            chr_r2_cache_dir = os.path.join(self.r2_cache_dir, f'chr{self.chr}')
-            self.chr_r2_cache_dir = chr_r2_cache_dir
-            if not os.path.exists(os.path.join(chr_r2_cache_dir, 'combined_r2_matrix.npz')):
-                logger.warning(
-                    f'No r2 cache found for chr{self.chr}, will generate r2 cache for this chromosome, first time may take a while')
-                os.makedirs(chr_r2_cache_dir, exist_ok=True, mode=0o777, )
-                self.generate_r2_cache = True
-            else:
-                logger.info(f'Found r2 cache for chr{self.chr}, will use r2 cache for this chromosome')
-
-    def compute_ldscore(self):
-        """
-        Compute LD scores.
-        """
-        start_time = time.time()
-        if self.chr == None:
-            for chr in range(1, 23):
-                logger.info(f'Computing LD scores for chr{chr}')
-                self.compute_ldscore_chr(chr=chr)
-                logger.info(f'Finished computing LD scores for chr{chr}')
-        else:
-            logger.info(f'Computing LD scores for chr{self.chr}')
-            self.compute_ldscore_chr(chr=self.chr)
-            logger.info(f'Finished computing LD scores for chr{self.chr}')
-        end_time = time.time()
-        logger.info(f'Finished computing LD scores, time elapsed: {(end_time - start_time) / 60} minutes')
-
-    def compute_ldscore_chunk(self, annot_file, ld_score_file, M_file, M_5_file, geno_array: PlinkBEDFileWithR2Cache,
-                              block_left, snp):
-        """
-        Compute and save LD scores for each chunk
-        :param annot_file: Path to the annotation file
-        :param ld_score_file: Path to the LD score file
-        :param M_file: Path to the M file
-        :param M_5_file: Path to the M_5_50 file
-        :param geno_array: Genotype array
-        :param block_left: Block left
-        :param snp: SNP to be kept
-        :return: None
-        """
-        annot_df = pd.read_feather(annot_file)
-        n_annot, ma = len(annot_df.columns) - 6, len(annot_df)
-
-        # print("Read {A} annotations for {M} SNPs from {f}".format(f=annot_file, A=n_annot, M=ma))
-        annot_matrix = np.array(annot_df.iloc[:, 6:])
-        annot_colnames = annot_df.columns[6:]
-
-        # Reset the SNP point
-        geno_array.__restart__()
-
-        # Compute annotated LD score
-        if self.chr_r2_cache_dir is None:
-            lN_df = pd.DataFrame(geno_array.ldScoreVarBlocks(block_left, 50, annot=annot_matrix))
-        else:
-            lN_df = pd.DataFrame(self.get_ldscore_use_cache(annot_matrix))
-
-        ldscore = pd.concat([annot_df.iloc[:, 0:6], lN_df], axis=1)
-        ldscore.columns = annot_df.columns
-
-        # Keep the targeted SNPs
-        if not snp is None:
-            ldscore = ldscore.loc[ldscore.SNP.isin(snp)]
-
-        # Save the LD score annotations
-        ldscore = ldscore.reset_index()
-        ldscore.drop(columns=['index'], inplace=True)
-        ldscore.to_feather(ld_score_file)
-
-        # Compute the .M (.M_5_50) file
-        M = np.atleast_1d(np.squeeze(np.asarray(np.sum(annot_matrix, axis=0))))
-        ii = geno_array.maf > 0.05
-        M_5_50 = np.atleast_1d(np.squeeze(np.asarray(np.sum(annot_matrix[ii, :], axis=0))))
-
-        # Save the sum of score annotations (all and maf > 0.05)
-        np.savetxt(M_file, M, delimiter='\t')
-        np.savetxt(M_5_file, M_5_50, delimiter='\t')
-
-    def get_ldscore_use_cache(self, annot_matrix, ):
-        if self.use_gpu:
-            logger.debug('Using GPU to compute LD score')
-            annot_matrix = cp.asarray(annot_matrix, dtype=cp.float32)
-            for i, r2_matrix_chunk in enumerate(self.r2_matrix_chunk_list):
-                r2_matrix_chunk = cp.sparse.csr_matrix(r2_matrix_chunk, dtype=cp.float32)
-                lN_chunk = cp.asnumpy(r2_matrix_chunk @ annot_matrix)
-                # convert to float16
-                lN_chunk = lN_chunk.astype(np.float16)
-                if i == 0:
-                    lN = lN_chunk
-                else:
-                    lN = np.concatenate([lN, lN_chunk], axis=0)
-        else:
-            logger.debug('Using CPU to compute LD score')
-            for i, r2_matrix_chunk in enumerate(self.r2_matrix_chunk_list):
-                lN_chunk = r2_matrix_chunk @ annot_matrix
-                # convert to float16
-                lN_chunk = lN_chunk.astype(np.float16)
-                if i == 0:
-                    lN = lN_chunk
-                else:
-                    lN = np.concatenate([lN, lN_chunk], axis=0)
-        return lN
-
-    def compute_ldscore_chr(self, chr):
-        PlinkBIMFile = ID_List_Factory(['CHR', 'SNP', 'CM', 'BP', 'A1', 'A2'], 1, '.bim', usecols=[0, 1, 2, 3, 4, 5])
-        PlinkFAMFile = ID_List_Factory(['IID'], 0, '.fam', usecols=[1])
-
-        bfile = f"{self.bfile_root}.{chr}"
-        #
-        # Load bim file
-        snp_file, snp_obj = bfile + '.bim', PlinkBIMFile
-        array_snps = snp_obj(snp_file)
-        m = len(array_snps.IDList)
-        print(f'Read list of {m} SNPs from {snp_file}')
-        #
-        # Load fam
-        ind_file, ind_obj = bfile + '.fam', PlinkFAMFile
-        array_indivs = ind_obj(ind_file)
-        n = len(array_indivs.IDList)
-        print(f'Read list of {n} individuals from {ind_file}')
-        #
-        # Load genotype array
-        array_file, array_obj = bfile + '.bed', PlinkBEDFileWithR2Cache
-        geno_array = array_obj(array_file, n, array_snps, keep_snps=None, keep_indivs=None, mafMin=None)
-
-        # Load the snp to be print
-        if not self.keep_snp is None:
-            snp = pd.read_csv(f'{self.keep_snp}.{chr}.snp', header=None)[0].to_list()
-            num_snp = len(snp)
-            print(f'Loading {num_snp} SNPs')
-        else:
-            snp = None
-
-        # Load the annotations of the baseline
-        if self.ld_wind_unit == 'SNP':
-            max_dist = self.ld_wind
-            coords = np.array(range(geno_array.m))
-        elif self.ld_wind_unit == 'BP':
-            max_dist = self.ld_wind * 1000
-            coords = np.array(array_snps.df['BP'])[geno_array.kept_snps]
-        elif self.ld_wind_unit == 'CM':
-            max_dist = self.ld_wind
-            coords = np.array(array_snps.df['CM'])[geno_array.kept_snps]
-        block_left = getBlockLefts(coords, max_dist)
-        if self.generate_r2_cache:
-            logger.info(f'Generating r2 cache for chr{chr}, this may take a while')
-            geno_array.compute_r2_cache(block_left,
-                                        Path(self.chr_r2_cache_dir))
-            logger.info(f'Finished generating r2 cache for chr{chr}')
-        if self.chr_r2_cache_dir is not None:
-            logger.info('Loading r2 cache')
-            r2_matrix = geno_array.load_combined_r2_matrix(cached_r2_matrix_dir=self.chr_r2_cache_dir)
-            self.r2_matrix_chunk_list = [r2_matrix[i:i + self.config.snps_per_chunk, :] for i in
-                                         range(0, r2_matrix.shape[0], self.config.snps_per_chunk)]
-            logger.info('Finished loading r2 cache')
-        # Set the baseline root
-        annot_file = f'{self.annot_root}/baseline/baseline.{chr}.feather'
-        ld_score_file = f'{self.annot_root}/baseline/baseline.{chr}.l2.ldscore.feather'
-        M_file = f'{self.annot_root}/baseline/baseline.{chr}.l2.M'
-        M_5_file = f'{self.annot_root}/baseline/baseline.{chr}.l2.M_5_50'
-
-        # Compute annotations of the baseline
-        print(f"Computing LD score for baseline annotations of chr{chr}")
-        self.compute_ldscore_chunk(annot_file, ld_score_file, M_file, M_5_file, geno_array, block_left, snp)
-
-        # Load annotations of chunks
-        bar = IncrementalBar(f"Computing LD scores for spatial data annotations of chr{chr}", max=self.const_max_size)
-        bar.check_tty = False
-        for chunk_index in range(1, self.const_max_size + 1):
-            # Set the file root
-            annot_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.feather'
-            ld_score_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.l2.ldscore.feather'
-            M_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.l2.M'
-            M_5_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.l2.M_5_50'
-
-            # Compute annotations of the current chunk
-            self.compute_ldscore_chunk(annot_file, ld_score_file, M_file, M_5_file, geno_array, block_left, snp)
-
-            bar.next()
-
-        bar.finish()
-
-
-
-def add_make_annotation_args(parser):
-    parser.add_argument('--input_feather_file', required=True, type=str, help='Input feather file for marker genes score (output of gsMap latent_to_gene)')
-    parser.add_argument('--output_dir', required=True, type=str, help='Output directory to save the SNP annotation files')
-    parser.add_argument('--sample_name', type=str, help='Name of the sample', required=True)
-    parser.add_argument('--gtf_annotation_file', default=None, type=str, help='Path to the GTF file', required=True)
-    parser.add_argument('--bfile_root', default=None, type=str, help='Bfile root for LD score', required=True)
-    parser.add_argument('--baseline_annotation', default=None, type=str, help='Baseline annotation')
-    parser.add_argument('--keep_snp_root', default=None, type=str,
-                        help='Only keep these SNP file after calculating LD score')
-    parser.add_argument('--chr', default=None, type=int, help='Chromosome ID', )
-    parser.add_argument('--window_size', default=50000, type=int,
-                        help='Window size for SNP annotation')
-    parser.add_argument('--cells_per_chunk', default=500, type=int,
-                        help='Chunk size for number of cells for batch processing')
-    parser.add_argument('--ld_wind', default=1, type=float)
-    parser.add_argument('--ld_wind_unit', default='CM', type=str, choices=['CM', 'BP', 'SNP'],
-                        help='LD window size unit')
-    parser.add_argument('--r2_cache_dir', default=None, type=str, help='Directory for r2 cache')
-    parser.add_argument('--use_gpu', action='store_true', help='Whether to use GPU to compute LD score')
-    parser.add_argument('--snps_per_chunk', default=50_000, type=int,
-                        help='Chunk size for number of SNPs for batch processing')
-
-
-# Defin the Container for plink files
-
-def run_make_annotation(args: MakeAnnotationConfig):
-
-    snp_annotate = Snp_Annotator(mk_score_file=args.input_feather_file,
-                                 gtf_file=args.gtf_file,
-                                 bfile_root=args.bfile_root,
-                                 annot_root=Path(args.output_dir),
-                                 annot_name=args.sample_name,
-                                 chr=args.chr,
-                                 base_root=args.baseline_annotation,
-                                 window_size=args.window_size,
-                                 const_max_size=args.cells_per_chunk
-                                 )
-    const_max_size = snp_annotate.annotate()
-    ldscore_generate = LDscore_Generator(
-        args, const_max_size
-    )
-    ldscore_generate.compute_ldscore()
+import argparse
+import logging
+import os
+import pprint
+import time
+from pathlib import Path
+
+
+import numpy as np
+import pandas as pd
+import pyranges as pr
+from progress.bar import IncrementalBar
+
+from gsMap.utils.generate_r2_matrix import PlinkBEDFileWithR2Cache, getBlockLefts, ID_List_Factory
+
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.DEBUG)
+handler = logging.StreamHandler()
+handler.setFormatter(logging.Formatter(
+    '[{asctime}] {levelname:8s} {filename} {message}', style='{'))
+logger.addHandler(handler)
+from dataclasses import dataclass, field
+from typing import Optional
+try:
+    import cupy as cp
+    pool = cp.cuda.MemoryPool(cp.cuda.malloc_async)
+    cp.cuda.set_allocator(pool.malloc)
+except ImportError:
+    logger.warning('Cupy not found, will not use GPU to compute LD score')
+    cp = None
+@dataclass
+class MakeAnnotationConfig:
+    input_feather_file: str
+    output_dir: str
+    sample_name: str
+    gtf_file: Optional[str] = None
+    bfile_root: Optional[str] = None
+    baseline_annotation: Optional[str] = None
+    keep_snp_root: Optional[str] = None
+    chr: Optional[int] = None
+    window_size: int = 50000
+    cells_per_chunk: int = 500
+    ld_wind: float = 1.0
+    ld_wind_unit: str = field(default='CM', metadata={'choices': ['CM', 'BP', 'SNP']})
+    r2_cache_dir: Optional[str] = None
+    use_gpu: bool = False
+    snps_per_chunk: int = 50_000
+
+    def __post_init__(self):
+        if self.ld_wind_unit not in self.__dataclass_fields__['ld_wind_unit'].metadata['choices']:
+            raise ValueError(f"Invalid ld_wind_unit: {self.ld_wind_unit}. Choose from 'CM', 'BP', or 'SNP'.")
+
+
+class Snp_Annotator:
+    """
+    1. Annotate SNPs based on score of genes.
+    2. Add baseline annotations.
+    """
+
+    def __init__(self, mk_score_file, gtf_file, bfile_root, annot_root, annot_name, chr=None, base_root=None,
+                 window_size=50000, const_max_size=100):
+        #
+        # marker score
+        self.mk_score_file = mk_score_file
+        self.mk_score = self.load_marker_score()
+        #
+        # chunk cells
+        # self.const_max_size = const_max_size
+        self.n_cells = len(self.mk_score.columns)
+        self.max_chunk = const_max_size
+        # self.max_chunk = floor(self.n_cells / self.const_max_size)
+        #
+        # gtf data
+        self.gtf_file = gtf_file
+        self.window_size = window_size
+        self.gtf_pr = self.load_gtf(mk_score=self.mk_score)
+        #
+        self.bfile_root = bfile_root
+        self.annot_root = annot_root
+        self.base_root = base_root
+        self.chr = chr
+
+        self.data_name = annot_name
+
+    #
+    def load_marker_score(self):
+        """
+        Load marker scores of each cell.
+        """
+        mk_score = pd.read_feather(self.mk_score_file).set_index('HUMAN_GENE_SYM').rename_axis('gene_name')
+        mk_score.insert(0, 'all_gene', 1)
+        return mk_score
+
+    #
+    def load_gtf(self, mk_score):
+        """
+        Load the gene annotation file (gtf).
+        """
+        print("Loading gtf data")
+        #
+        # Load GTF file
+        gtf = pr.read_gtf(self.gtf_file)
+        gtf = gtf.df
+        #
+        # Select the common genes
+        gtf = gtf[gtf['Feature'] == 'gene']
+        common_gene = np.intersect1d(mk_score.index, gtf.gene_name)
+        #
+        gtf = gtf[gtf.gene_name.isin(common_gene)]
+        mk_score = mk_score[mk_score.index.isin(common_gene)]
+        #
+        # Remove duplicated lines
+        gtf = gtf.drop_duplicates(subset='gene_name', keep="first")
+        #
+        # Process the GTF (open 100-KB window: Tss - Ted)
+        gtf_bed = gtf[['Chromosome', 'Start', 'End', 'gene_name', 'Strand']].copy()
+        gtf_bed.loc[:, 'TSS'] = gtf_bed['Start']
+        gtf_bed.loc[:, 'TED'] = gtf_bed['End']
+
+        gtf_bed.loc[:, 'Start'] = gtf_bed['TSS'] - self.window_size
+        gtf_bed.loc[:, 'End'] = gtf_bed['TED'] + self.window_size
+        gtf_bed.loc[gtf_bed['Start'] < 0, 'Start'] = 0
+        #
+        # Correct the negative strand
+        tss_neg = gtf_bed.loc[gtf_bed['Strand'] == '-', 'TSS']
+        ted_neg = gtf_bed.loc[gtf_bed['Strand'] == '-', 'TED']
+        gtf_bed.loc[gtf_bed['Strand'] == '-', 'TSS'] = ted_neg
+        gtf_bed.loc[gtf_bed['Strand'] == '-', 'TED'] = tss_neg
+        gtf_bed = gtf_bed.drop('Strand', axis=1)
+        #
+        # Transform the GTF to PyRanges
+        gtf_pr = pr.PyRanges(gtf_bed)
+        return gtf_pr
+
+    #
+    def load_baseline(self, chr):
+        """
+        Load baseline annotations.
+        """
+        baseline = pd.read_csv(f'{self.base_root}.{chr}.annot.gz', sep='\t')
+        baseline.drop(['CHR', 'BP', 'CM'], axis=1, inplace=True)
+        return baseline
+
+    # -
+    def Load_bim(self, chr):
+        """
+        Load bim files.
+        """
+        bim_file = f'{self.bfile_root}.{chr}.bim'
+        bim = pd.read_csv(bim_file, sep='\t', header=None)
+        bim.columns = ["CHR", "SNP", "CM", "BP", "A1", "A2"]
+        #
+        # Transform bim to PyRanges
+        bim_pr = bim.copy()
+        bim_pr.columns = ["Chromosome", "SNP", "CM", "Start", "A1", "A2"]
+        bim_pr['End'] = bim_pr['Start']
+        bim_pr = pr.PyRanges(bim_pr)
+        bim_pr.Chromosome = f'chr{chr}'
+        return bim_pr, bim
+
+    # -
+    def Overlaps_gtf_bim(self, bim_pr):
+        """
+        Find overlaps between gtf and bim file.
+        """
+        # Select the overlapped regions (SNPs in gene windows)
+        overlaps = self.gtf_pr.join(bim_pr)
+        overlaps = overlaps.df
+        overlaps['Distance'] = np.abs(overlaps['Start_b'] - overlaps['TSS'])
+        overlaps_small = overlaps.copy()
+        overlaps_small = overlaps_small.loc[overlaps_small.groupby('SNP').Distance.idxmin()]
+        return overlaps_small
+
+    # -
+    def map_baseline(self, snp_score, baseline, chr):
+        """
+        Generate the baseline annotations for SNPs.
+        """
+
+        header = snp_score.columns[0:6].to_list()
+
+        if baseline is None:
+            print(f'Baseline annotations of chr{chr} are not provided, using uniform annotations for genes and SNPs')
+            baseline_score = snp_score[header + ['all_gene']].copy()
+            baseline_score.loc[:, 'base'] = 1
+
+        else:
+            print(f'Mapping baseline annotations of chr{chr}')
+            snp_score_baseline = pd.merge(snp_score, baseline, how='left', on='SNP').fillna(0).copy()
+
+            baseline_score = snp_score_baseline[header + ['all_gene'] + baseline.columns.to_list()]
+            baseline_score = baseline_score.loc[:, ~baseline_score.columns.duplicated()].copy()
+
+        # Create the folder (for baseline annotation)
+        file_base_root = f'{self.annot_root}/baseline'
+        if not os.path.exists(file_base_root):
+            os.makedirs(file_base_root, mode=0o777, exist_ok=True)
+
+            # Save baseline annotations (in parquet format)
+        file_base = f'{file_base_root}/baseline.{chr}.feather'
+        baseline_score.to_feather(file_base)
+
+        return 0
+
+    # -
+    def annotate_chr(self, chr):
+        """
+        Annotate SNPs of each chr.
+        """
+        # Load the baseline file
+        baseline = None
+        if self.base_root is not None:
+            baseline = self.load_baseline(chr)
+
+        # Load the bim file
+        bim_pr, bim = self.Load_bim(chr)
+
+        # Find overlapping
+        overlaps_small = self.Overlaps_gtf_bim(bim_pr)
+
+        # Do annotations
+        all_chunks = int(np.ceil(self.n_cells / self.max_chunk))
+        bar = IncrementalBar(f'Mapping the gene marker scores to SNPs in chr{chr}', max=all_chunks)
+        bar.check_tty = False
+
+        # Preprocess bim outside the loop as it doesn't change
+        anno_template = bim[["CHR", "BP", "SNP", "CM"]]
+
+        for chunk_index, left in enumerate(range(0, self.n_cells, self.max_chunk), start=1):
+            right = min(left + self.max_chunk, self.n_cells)
+            mk_score_current = self.mk_score.iloc[:, left:right]
+
+            # Process marker scores for SNPs
+            anno = anno_template.copy()
+            merged_data = overlaps_small[['SNP', 'gene_name', 'TSS']].merge(mk_score_current, on='gene_name',
+                                                                            how='left')
+            snp_score = pd.merge(anno, merged_data, how='left', on='SNP').fillna(0)
+            snp_score = snp_score.rename(columns={'gene_name': 'Gene'})
+            snp_score.loc[snp_score.Gene == 0, 'Gene'] = 'None'
+
+            # Process baseline annotations for the first chunk
+            if chunk_index == 1:
+                self.map_baseline(snp_score, baseline, chr)
+                snp_score = snp_score.drop('all_gene', axis=1)
+
+            # Create the folder and save SNP annotations
+            file_root = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}'
+            os.makedirs(file_root, mode=0o777, exist_ok=True)
+            file_anno = f'{file_root}/{self.data_name}.{chr}.feather'
+            snp_score.to_feather(file_anno)
+
+            bar.next()
+
+        bar.finish()
+
+        return all_chunks
+
+    #
+    def annotate(self):
+        """
+        Perform SNP annotations for each chromosome.
+        """
+        if self.chr == None:
+            for chr in range(1, 23):
+                const_max_size = self.annotate_chr(chr=chr)
+        else:
+            const_max_size = self.annotate_chr(chr=self.chr)
+
+        return const_max_size
+
+
+class LDscore_Generator:
+    def __init__(self, make_annotation_config: MakeAnnotationConfig, const_max_size):
+        self.bfile_root = make_annotation_config.bfile_root
+        self.annot_root = Path(make_annotation_config.output_dir)
+        self.const_max_size = const_max_size
+        self.data_name = make_annotation_config.sample_name
+        self.chr = make_annotation_config.chr
+        self.ld_wind = make_annotation_config.ld_wind
+        self.ld_wind_unit = make_annotation_config.ld_wind_unit
+        self.keep_snp = make_annotation_config.keep_snp_root
+        self.r2_cache_dir = make_annotation_config.r2_cache_dir
+        self.use_gpu = make_annotation_config.use_gpu
+        self.config = make_annotation_config
+        self.generate_r2_cache = False
+
+        # Set the r2 cache
+        if self.r2_cache_dir is None:
+            logger.info('No r2 cache directory specified, will not use r2 cache')
+            self.chr_r2_cache_dir = None
+        else:
+            assert self.chr is not None, 'Must specify chr when using r2 cache'
+            chr_r2_cache_dir = os.path.join(self.r2_cache_dir, f'chr{self.chr}')
+            self.chr_r2_cache_dir = chr_r2_cache_dir
+            if not os.path.exists(os.path.join(chr_r2_cache_dir, 'combined_r2_matrix.npz')):
+                logger.warning(
+                    f'No r2 cache found for chr{self.chr}, will generate r2 cache for this chromosome, first time may take a while')
+                os.makedirs(chr_r2_cache_dir, exist_ok=True, mode=0o777, )
+                self.generate_r2_cache = True
+            else:
+                logger.info(f'Found r2 cache for chr{self.chr}, will use r2 cache for this chromosome')
+
+    def compute_ldscore(self):
+        """
+        Compute LD scores.
+        """
+        start_time = time.time()
+        if self.chr == None:
+            for chr in range(1, 23):
+                logger.info(f'Computing LD scores for chr{chr}')
+                self.compute_ldscore_chr(chr=chr)
+                logger.info(f'Finished computing LD scores for chr{chr}')
+        else:
+            logger.info(f'Computing LD scores for chr{self.chr}')
+            self.compute_ldscore_chr(chr=self.chr)
+            logger.info(f'Finished computing LD scores for chr{self.chr}')
+        end_time = time.time()
+        logger.info(f'Finished computing LD scores, time elapsed: {(end_time - start_time) / 60} minutes')
+
+    def compute_ldscore_chunk(self, annot_file, ld_score_file, M_file, M_5_file, geno_array: PlinkBEDFileWithR2Cache,
+                              block_left, snp):
+        """
+        Compute and save LD scores for each chunk
+        :param annot_file: Path to the annotation file
+        :param ld_score_file: Path to the LD score file
+        :param M_file: Path to the M file
+        :param M_5_file: Path to the M_5_50 file
+        :param geno_array: Genotype array
+        :param block_left: Block left
+        :param snp: SNP to be kept
+        :return: None
+        """
+        annot_df = pd.read_feather(annot_file)
+        n_annot, ma = len(annot_df.columns) - 6, len(annot_df)
+
+        # print("Read {A} annotations for {M} SNPs from {f}".format(f=annot_file, A=n_annot, M=ma))
+        annot_matrix = np.array(annot_df.iloc[:, 6:])
+        annot_colnames = annot_df.columns[6:]
+
+        # Reset the SNP point
+        geno_array.__restart__()
+
+        # Compute annotated LD score
+        if self.chr_r2_cache_dir is None:
+            lN_df = pd.DataFrame(geno_array.ldScoreVarBlocks(block_left, 50, annot=annot_matrix))
+        else:
+            lN_df = pd.DataFrame(self.get_ldscore_use_cache(annot_matrix))
+
+        ldscore = pd.concat([annot_df.iloc[:, 0:6], lN_df], axis=1)
+        ldscore.columns = annot_df.columns
+
+        # Keep the targeted SNPs
+        if not snp is None:
+            ldscore = ldscore.loc[ldscore.SNP.isin(snp)]
+
+        # Save the LD score annotations
+        ldscore = ldscore.reset_index()
+        ldscore.drop(columns=['index'], inplace=True)
+        ldscore.to_feather(ld_score_file)
+
+        # Compute the .M (.M_5_50) file
+        M = np.atleast_1d(np.squeeze(np.asarray(np.sum(annot_matrix, axis=0))))
+        ii = geno_array.maf > 0.05
+        M_5_50 = np.atleast_1d(np.squeeze(np.asarray(np.sum(annot_matrix[ii, :], axis=0))))
+
+        # Save the sum of score annotations (all and maf > 0.05)
+        np.savetxt(M_file, M, delimiter='\t')
+        np.savetxt(M_5_file, M_5_50, delimiter='\t')
+
+    def get_ldscore_use_cache(self, annot_matrix, ):
+        if self.use_gpu:
+            logger.debug('Using GPU to compute LD score')
+            annot_matrix = cp.asarray(annot_matrix, dtype=cp.float32)
+            for i, r2_matrix_chunk in enumerate(self.r2_matrix_chunk_list):
+                r2_matrix_chunk = cp.sparse.csr_matrix(r2_matrix_chunk, dtype=cp.float32)
+                lN_chunk = cp.asnumpy(r2_matrix_chunk @ annot_matrix)
+                # convert to float16
+                lN_chunk = lN_chunk.astype(np.float16)
+                if i == 0:
+                    lN = lN_chunk
+                else:
+                    lN = np.concatenate([lN, lN_chunk], axis=0)
+        else:
+            logger.debug('Using CPU to compute LD score')
+            for i, r2_matrix_chunk in enumerate(self.r2_matrix_chunk_list):
+                lN_chunk = r2_matrix_chunk @ annot_matrix
+                # convert to float16
+                lN_chunk = lN_chunk.astype(np.float16)
+                if i == 0:
+                    lN = lN_chunk
+                else:
+                    lN = np.concatenate([lN, lN_chunk], axis=0)
+        return lN
+
+    def compute_ldscore_chr(self, chr):
+        PlinkBIMFile = ID_List_Factory(['CHR', 'SNP', 'CM', 'BP', 'A1', 'A2'], 1, '.bim', usecols=[0, 1, 2, 3, 4, 5])
+        PlinkFAMFile = ID_List_Factory(['IID'], 0, '.fam', usecols=[1])
+
+        bfile = f"{self.bfile_root}.{chr}"
+        #
+        # Load bim file
+        snp_file, snp_obj = bfile + '.bim', PlinkBIMFile
+        array_snps = snp_obj(snp_file)
+        m = len(array_snps.IDList)
+        print(f'Read list of {m} SNPs from {snp_file}')
+        #
+        # Load fam
+        ind_file, ind_obj = bfile + '.fam', PlinkFAMFile
+        array_indivs = ind_obj(ind_file)
+        n = len(array_indivs.IDList)
+        print(f'Read list of {n} individuals from {ind_file}')
+        #
+        # Load genotype array
+        array_file, array_obj = bfile + '.bed', PlinkBEDFileWithR2Cache
+        geno_array = array_obj(array_file, n, array_snps, keep_snps=None, keep_indivs=None, mafMin=None)
+
+        # Load the snp to be print
+        if not self.keep_snp is None:
+            snp = pd.read_csv(f'{self.keep_snp}.{chr}.snp', header=None)[0].to_list()
+            num_snp = len(snp)
+            print(f'Loading {num_snp} SNPs')
+        else:
+            snp = None
+
+        # Load the annotations of the baseline
+        if self.ld_wind_unit == 'SNP':
+            max_dist = self.ld_wind
+            coords = np.array(range(geno_array.m))
+        elif self.ld_wind_unit == 'BP':
+            max_dist = self.ld_wind * 1000
+            coords = np.array(array_snps.df['BP'])[geno_array.kept_snps]
+        elif self.ld_wind_unit == 'CM':
+            max_dist = self.ld_wind
+            coords = np.array(array_snps.df['CM'])[geno_array.kept_snps]
+        block_left = getBlockLefts(coords, max_dist)
+        if self.generate_r2_cache:
+            logger.info(f'Generating r2 cache for chr{chr}, this may take a while')
+            geno_array.compute_r2_cache(block_left,
+                                        Path(self.chr_r2_cache_dir))
+            logger.info(f'Finished generating r2 cache for chr{chr}')
+        if self.chr_r2_cache_dir is not None:
+            logger.info('Loading r2 cache')
+            r2_matrix = geno_array.load_combined_r2_matrix(cached_r2_matrix_dir=self.chr_r2_cache_dir)
+            self.r2_matrix_chunk_list = [r2_matrix[i:i + self.config.snps_per_chunk, :] for i in
+                                         range(0, r2_matrix.shape[0], self.config.snps_per_chunk)]
+            logger.info('Finished loading r2 cache')
+        # Set the baseline root
+        annot_file = f'{self.annot_root}/baseline/baseline.{chr}.feather'
+        ld_score_file = f'{self.annot_root}/baseline/baseline.{chr}.l2.ldscore.feather'
+        M_file = f'{self.annot_root}/baseline/baseline.{chr}.l2.M'
+        M_5_file = f'{self.annot_root}/baseline/baseline.{chr}.l2.M_5_50'
+
+        # Compute annotations of the baseline
+        print(f"Computing LD score for baseline annotations of chr{chr}")
+        self.compute_ldscore_chunk(annot_file, ld_score_file, M_file, M_5_file, geno_array, block_left, snp)
+
+        # Load annotations of chunks
+        bar = IncrementalBar(f"Computing LD scores for spatial data annotations of chr{chr}", max=self.const_max_size)
+        bar.check_tty = False
+        for chunk_index in range(1, self.const_max_size + 1):
+            # Set the file root
+            annot_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.feather'
+            ld_score_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.l2.ldscore.feather'
+            M_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.l2.M'
+            M_5_file = f'{self.annot_root}/{self.data_name}_chunk{chunk_index}/{self.data_name}.{chr}.l2.M_5_50'
+
+            # Compute annotations of the current chunk
+            self.compute_ldscore_chunk(annot_file, ld_score_file, M_file, M_5_file, geno_array, block_left, snp)
+
+            bar.next()
+
+        bar.finish()
+
+
+
+def add_make_annotation_args(parser):
+    parser.add_argument('--input_feather_file', required=True, type=str, help='Input feather file for marker genes score (output of gsMap latent_to_gene)')
+    parser.add_argument('--output_dir', required=True, type=str, help='Output directory to save the SNP annotation files')
+    parser.add_argument('--sample_name', type=str, help='Name of the sample', required=True)
+    parser.add_argument('--gtf_annotation_file', default=None, type=str, help='Path to the GTF file', required=True)
+    parser.add_argument('--bfile_root', default=None, type=str, help='Bfile root for LD score', required=True)
+    parser.add_argument('--baseline_annotation', default=None, type=str, help='Baseline annotation')
+    parser.add_argument('--keep_snp_root', default=None, type=str,
+                        help='Only keep these SNP file after calculating LD score')
+    parser.add_argument('--chr', default=None, type=int, help='Chromosome ID', )
+    parser.add_argument('--window_size', default=50000, type=int,
+                        help='Window size for SNP annotation')
+    parser.add_argument('--cells_per_chunk', default=500, type=int,
+                        help='Chunk size for number of cells for batch processing')
+    parser.add_argument('--ld_wind', default=1, type=float)
+    parser.add_argument('--ld_wind_unit', default='CM', type=str, choices=['CM', 'BP', 'SNP'],
+                        help='LD window size unit')
+    parser.add_argument('--r2_cache_dir', default=None, type=str, help='Directory for r2 cache')
+    parser.add_argument('--use_gpu', action='store_true', help='Whether to use GPU to compute LD score')
+    parser.add_argument('--snps_per_chunk', default=50_000, type=int,
+                        help='Chunk size for number of SNPs for batch processing')
+
+
+# Defin the Container for plink files
+
+def run_make_annotation(args: MakeAnnotationConfig):
+
+    snp_annotate = Snp_Annotator(mk_score_file=args.input_feather_file,
+                                 gtf_file=args.gtf_file,
+                                 bfile_root=args.bfile_root,
+                                 annot_root=Path(args.output_dir),
+                                 annot_name=args.sample_name,
+                                 chr=args.chr,
+                                 base_root=args.baseline_annotation,
+                                 window_size=args.window_size,
+                                 const_max_size=args.cells_per_chunk
+                                 )
+    const_max_size = snp_annotate.annotate()
+    ldscore_generate = LDscore_Generator(
+        args, const_max_size
+    )
+    ldscore_generate.compute_ldscore()