gsMap 1.72.3__py3-none-any.whl → 1.73.0__py3-none-any.whl

gsMap/utils/generate_r2_matrix.py

@@ -1,42 +1,7 @@
-from pathlib import Path
-
 import bitarray as ba
 import numpy as np
 import pandas as pd
-from scipy.sparse import csr_matrix, load_npz, save_npz
-from tqdm import tqdm, trange
-
-
-# Define the log class
-class Logger:
-    # -
-    def __init__(self, fh):
-        self.log_fh = open(fh, "w")
-
-    # -
-    def log(self, msg):
-        """
-        Print to log file and stdout.
-        """
-        print(msg, file=self.log_fh)
-        print(msg)
-
-    # -
-    def close(self):
-        self.log_fh.close()
-
-
-# Compute ld-score using cellular annotations
-def get_compression(fh):
-    """Which sort of compression should we use with read_csv?"""
-    if fh.endswith("gz"):
-        compression = "gzip"
-    elif fh.endswith("bz2"):
-        compression = "bz2"
-    else:
-        compression = None
-    # -
-    return compression
+from tqdm import tqdm
 
 
 # Define the reading functions
@@ -67,29 +32,17 @@ def ID_List_Factory(colnames, keepcol, fname_end, header=None, usecols=None):
             end = self.fname_end
             if end and not fname.endswith(end):
                 raise ValueError(f"{end} filename must end in {end}")
-            comp = get_compression(fname)
             self.df = pd.read_csv(
-                fname, header=self.header, usecols=self.usecols, sep=r"\s+", compression=comp
+                fname,
+                header=self.header,
+                usecols=self.usecols,
+                sep=r"\s+",
             )
             if self.colnames:
                 self.df.columns = self.colnames
             if self.keepcol is not None:
                 self.IDList = self.df.iloc[:, [self.keepcol]].astype("object")
 
-        # -
-        def loj(self, externalDf):
-            """
-            Perform a left outer join operation with the given external DataFrame.
-            """
-            r = externalDf.columns[0]
-            l = self.IDList.columns[0]
-            merge_df = externalDf.iloc[:, [0]]
-            merge_df["keep"] = True
-            z = pd.merge(self.IDList, merge_df, how="left", left_on=l, right_on=r, sort=False)
-            ii = z["keep"]
-            return np.nonzero(ii)[0]
-
-    # -
     return IDContainer
 
 
@@ -512,257 +465,25 @@ class PlinkBEDFile(GenotypeArrayInMemory):
         return Y
 
 
-class PlinkBEDFileWithR2Cache(PlinkBEDFile):
-    def compute_r2_cache(
-        self,
-        block_left,
-        output_cache_file_dir: Path,
-        chunk_size=500_000_000,
-        c=500,
-        r2_threshold=1e-4,
-        annot=None,
-    ):
-        func = np.square
-        snp_getter = self.nextSNPs
-        data, rows, cols = [], [], []
-
-        def add_rfuncAB(rfuncAB, l_A, l_B):
-            non_zero_indices = np.nonzero(rfuncAB > r2_threshold)
-            data.extend(rfuncAB[non_zero_indices])
-            rows.extend(l_A + non_zero_indices[0])
-            cols.extend(l_B + non_zero_indices[1])
-
-        # def add_rfuncAB(rfuncAB, l_A, l_B):
-        #     # not need select non zero indices
-        #     data.extend(rfuncAB.flatten())
-        #     rows.extend(l_A + np.repeat(np.arange(rfuncAB.shape[0]), rfuncAB.shape[1]))
-        #     cols.extend(l_B + np.tile(np.arange(rfuncAB.shape[1]), rfuncAB.shape[0]))
-
-        # def add_rfuncBB(rfuncBB, l_B):
-        #     non_zero_indices = np.nonzero(rfuncBB)
-        #     data.extend(rfuncBB[non_zero_indices])
-        #     rows.extend(l_B + non_zero_indices[0])
-        #     cols.extend(l_B + non_zero_indices[1])
-
-        def add_rfuncBB(rfuncBB, l_B):
-            non_zero_indices = np.nonzero(rfuncBB > r2_threshold)
-            data.extend(rfuncBB[non_zero_indices])
-            rows.extend(l_B + non_zero_indices[0])
-            cols.extend(l_B + non_zero_indices[1])
-            if len(data) > chunk_size:
-                # save the cache
-                print(f"Start saving the cache file: {output_cache_file_dir / f'{l_B}.npz'}")
-                r2_sparse_matrix = csr_matrix(
-                    (data, (rows, cols)), shape=(self.m, self.m), dtype="float16"
-                )
-                save_npz(output_cache_file_dir / f"{l_B}.npz", r2_sparse_matrix)
-                # reset the data
-                data.clear()
-                rows.clear()
-                cols.clear()
-
-        m, n = self.m, self.n
-        block_sizes = np.array(np.arange(m) - block_left)
-        block_sizes = np.ceil(block_sizes / c) * c
-        if annot is None:
-            annot = np.ones((m, 1))
-        else:
-            annot_m = annot.shape[0]
-            if annot_m != self.m:
-                raise ValueError("Incorrect number of SNPs in annot")
-        # -
-        # n_a = annot.shape[1]  # number of annotations
-        # cor_sum = np.zeros((m, n_a))
-        # b = index of first SNP for which SNP 0 is not included in LD Score
-        b = np.nonzero(block_left > 0)
-        if np.any(b):
-            b = b[0][0]
-        else:
-            b = m
-        b = int(np.ceil(b / c) * c)  # round up to a multiple of c
-        if b > m:
-            c = 1
-            b = m
-
-        l_A = 0  # l_A := index of leftmost SNP in matrix A
-        A = snp_getter(b)
-        rfuncAB = np.zeros((b, c))
-        rfuncBB = np.zeros((c, c))
-        # chunk inside of block
-        for l_B in np.arange(0, b, c):  # l_B := index of leftmost SNP in matrix B
-            B = A[:, l_B : l_B + c]
-            # ld matrix
-            np.dot(A.T, B / n, out=rfuncAB)
-            # ld matrix square
-            rfuncAB = func(rfuncAB)
-            add_rfuncAB(rfuncAB, l_A, l_B)
-            # cor_sum[l_A:l_A + b, :] += np.dot(rfuncAB, annot[l_B:l_B + c, :])
-
-        # chunk to right of block
-        b0 = b
-        md = int(c * np.floor(m / c))
-        end = md + 1 if md != m else md
-        for l_B in trange(b0, end, c, desc=f"Compute r2 cache for {output_cache_file_dir.name}"):
-            # check if the annot matrix is all zeros for this block + chunk
-            # this happens w/ sparse categories (i.e., pathways)
-            # update the block
-            old_b = b
-            b = int(block_sizes[l_B])
-            if l_B > b0 and b > 0:
-                # block_size can't increase more than c
-                # block_size can't be less than c unless it is zero
-                # both of these things make sense
-                A = np.hstack((A[:, old_b - b + c : old_b], B))
-                l_A += old_b - b + c
-            elif l_B == b0 and b > 0:
-                A = A[:, b0 - b : b0]
-                l_A = b0 - b
-            elif b == 0:  # no SNPs to left in window, e.g., after a sequence gap
-                A = np.array(()).reshape((n, 0))
-                l_A = l_B
-            if l_B == md:
-                c = m - md
-                rfuncAB = np.zeros((b, c))
-                rfuncBB = np.zeros((c, c))
-            if b != old_b:
-                rfuncAB = np.zeros((b, c))
-            # -
-            B = snp_getter(c)
-            p1 = np.all(annot[l_A : l_A + b, :] == 0)
-            p2 = np.all(annot[l_B : l_B + c, :] == 0)
-            if p1 and p2:
-                continue
-            # -
-            np.dot(A.T, B / n, out=rfuncAB)
-            rfuncAB = func(rfuncAB)
-            # cor_sum[l_A:l_A + b, :] += np.dot(rfuncAB, annot[l_B:l_B + c, :])
-            # cor_sum[l_B:l_B + c, :] += np.dot(annot[l_A:l_A + b, :].T, rfuncAB).T
-            add_rfuncAB(rfuncAB, l_A, l_B)
-            add_rfuncAB(rfuncAB.T, l_B, l_A)
-            np.dot(B.T, B / n, out=rfuncBB)
-            rfuncBB = func(rfuncBB)
-            # cor_sum[l_B:l_B + c, :] += np.dot(rfuncBB, annot[l_B:l_B + c, :])
-            add_rfuncBB(rfuncBB, l_B)
-        if len(data) > 0:
-            # save remaining data
-            # save the cache
-            print(f"Start saving the cache file: {output_cache_file_dir / f'{l_B}.npz'}")
-            r2_sparse_matrix = csr_matrix((data, (rows, cols)), shape=(m, m), dtype="float16")
-            save_npz(output_cache_file_dir / f"{l_B}.npz", r2_sparse_matrix)
-        # combine the cache files
-        print(f"Start combining the cache files in {output_cache_file_dir}")
-        cached_r2_matrix_files = list(output_cache_file_dir.glob("*.npz"))
-        combined_r2_matrix_files = self.load_r2_matrix_from_cache_files(output_cache_file_dir)
-        # remove the cache files
-        for cached_r2_matrix_file in cached_r2_matrix_files:
-            cached_r2_matrix_file.unlink()
-        # save the combined r2 matrix
-        print(f"Start saving the combined r2 matrix in {output_cache_file_dir}")
-        combined_r2_matrix_file = output_cache_file_dir / "combined_r2_matrix.npz"
-        save_npz(combined_r2_matrix_file, combined_r2_matrix_files)
-
-    def get_ldscore_using_r2_cache(self, annot_matrix, cached_r2_matrix_dir):
-        """
-        Compute the r2 matrix multiplication with annot_matrix
-        """
-        # Compute the r2 matrix multiplication with annot_matrix
-        cached_r2_matrix_dir = Path(cached_r2_matrix_dir)
-        # iter the cached r2 matrix files
-        result_matrix = np.zeros((self.m, annot_matrix.shape[1]))
-        cached_r2_matrix_files = list(cached_r2_matrix_dir.glob("*.npz"))
-        assert len(cached_r2_matrix_files) > 0, (
-            f"No cached r2 matrix files in {cached_r2_matrix_dir}"
-            f"Please run the function compute_r2_cache first!"
-        )
-        for r2_matrix_file in tqdm(
-            cached_r2_matrix_files, desc=f"Compute ld score for {cached_r2_matrix_dir.name}"
-        ):
-            print(f"Compute r2 matrix multiplication for {r2_matrix_file}")
-            r2_matrix = load_npz(r2_matrix_file)
-            result_matrix += r2_matrix.dot(annot_matrix)
-        return result_matrix
-
-    def load_r2_matrix_from_cache_files(self, cached_r2_matrix_dir):
-        """
-        Load the r2 matrix from cache
-        """
-        cached_r2_matrix_dir = Path(cached_r2_matrix_dir)
-        # iter the cached r2 matrix files
-        cached_r2_matrix_files = list(cached_r2_matrix_dir.glob("*.npz"))
-        assert len(cached_r2_matrix_files) > 0, (
-            f"No cached r2 matrix files in {cached_r2_matrix_dir}"
-            f"Please run the function compute_r2_cache first!"
-        )
-        # load the r2 matrix
-        r2_matrix = load_npz(cached_r2_matrix_files[0])
-        for r2_matrix_file in tqdm(
-            cached_r2_matrix_files[1:], desc=f"Load r2 matrix from {cached_r2_matrix_dir.name}"
-        ):
-            print(f"Load r2 matrix from {r2_matrix_file}")
-            r2_matrix += load_npz(r2_matrix_file)
-        # to float16
-        r2_matrix = r2_matrix.astype("float16")
-        return r2_matrix
-
-    def load_combined_r2_matrix(self, cached_r2_matrix_dir):
-        """
-        Load the combined r2 matrix
-        """
-        combined_r2_matrix_file = Path(cached_r2_matrix_dir) / "combined_r2_matrix.npz"
-        assert combined_r2_matrix_file.exists(), (
-            f"No combined r2 matrix file in {cached_r2_matrix_dir}"
-            f"Should delete the cache files and run the function compute_r2_cache first!"
-        )
-        # load the r2 matrix
-        r2_matrix = load_npz(combined_r2_matrix_file)
-        # to float16
-        r2_matrix = r2_matrix.astype("float16")
-        return r2_matrix
-
-
 def load_bfile(bfile_chr_prefix):
     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])
 
-    snp_file, snp_obj = bfile_chr_prefix + ".bim", PlinkBIMFile
-    array_snps = snp_obj(snp_file)
-    m = len(array_snps.IDList)
-    print(f"Read list of {m} SNPs from {snp_file}")
-    #
+    snp_file = bfile_chr_prefix + ".bim"
+    array_snps = PlinkBIMFile(snp_file)
+
     # Load fam
-    ind_file, ind_obj = bfile_chr_prefix + ".fam", PlinkFAMFile
-    array_indivs = ind_obj(ind_file)
+    ind_file = bfile_chr_prefix + ".fam"
+    array_indivs = PlinkFAMFile(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_chr_prefix + ".bed", PlinkBEDFileWithR2Cache
-    geno_array = array_obj(
+    array_file = bfile_chr_prefix + ".bed"
+    geno_array = PlinkBEDFile(
         array_file, n, array_snps, keep_snps=None, keep_indivs=None, mafMin=None
     )
 
     return array_snps, array_indivs, geno_array
-
-
-def generate_r2_matrix_chr_cache(bfile_chr_prefix, ld_wind_cm, output_cache_file_dir):
-    # Load genotype array
-    array_snps, array_indivs, geno_array = load_bfile(bfile_chr_prefix)
-    # Compute block lefts
-    # block_left = getBlockLefts(geno_array.df[:, 3], ld_wind_cm)
-    # Compute LD score
-    # r2_matrix = geno_array.load_r2_matrix_from_cache(output_cache_file_dir)
-
-
-def generate_r2_matrix_cache(bfile_prefix, chromosome_list, r2_cache_dir, ld_wind_cm=1):
-    r2_cache_dir = Path(r2_cache_dir)
-
-    for chr in chromosome_list:
-        output_cache_file_prefix = r2_cache_dir / f"chr{chr}"
-        output_cache_file_prefix.mkdir(parents=True, exist_ok=True)
-        bfile_chr_prefix = bfile_prefix + "." + str(chr)
-        generate_r2_matrix_chr_cache(
-            bfile_chr_prefix, ld_wind_cm=ld_wind_cm, output_cache_file_dir=output_cache_file_prefix
-        )
-        print(f"Compute r2 matrix for chr{chr} done!")

gsMap/utils/regression_read.py

@@ -89,37 +89,6 @@ def which_compression(fh):
     return suffix, compression
 
 
-def _read_ref_ld(ld_file):
-    suffix = ".l2.ldscore"
-    file = ld_file
-    first_fh = f"{file}1{suffix}"
-    s, compression = which_compression(first_fh)
-    #
-    ldscore_array = []
-    print(f"Reading ld score annotations from {file}[1-22]{suffix}.{compression}")
-
-    for chr in range(1, 23):
-        file_chr = f"{file}{chr}{suffix}{s}"
-        #
-        if compression == "parquet":
-            x = pd.read_parquet(file_chr)
-        elif compression == "feather":
-            x = pd.read_feather(file_chr)
-        else:
-            x = pd.read_csv(file_chr, compression=compression, sep="\t")
-
-        x = x.sort_values(by=["CHR", "BP"])  # SEs will be wrong unless sorted
-
-        columns_to_drop = ["MAF", "CM", "Gene", "TSS", "CHR", "BP"]
-        columns_to_drop = [col for col in columns_to_drop if col in x.columns]
-        x = x.drop(columns_to_drop, axis=1)
-
-        ldscore_array.append(x)
-    #
-    ref_ld = pd.concat(ldscore_array, axis=0)
-    return ref_ld
-
-
 def _read_ref_ld_v2(ld_file):
     suffix = ".l2.ldscore"
     file = ld_file
@@ -185,23 +154,6 @@ def M(fh, common=False):
     return np.array(M_array).reshape((1, len(M_array)))
 
 
-def _check_variance(M_annot, ref_ld):
-    """
-    Remove zero-variance LD Scores.
-    """
-    ii = ref_ld.iloc[:, 1:].var() == 0  # NB there is a SNP column here
-    if ii.all():
-        raise ValueError("All LD Scores have zero variance.")
-    else:
-        print("Removing partitioned LD Scores with zero variance.")
-        ii_snp = np.array([True] + list(~ii))
-        ii_m = np.array(~ii)
-        ref_ld = ref_ld.iloc[:, ii_snp]
-        M_annot = M_annot[:, ii_m]
-    # -
-    return M_annot, ref_ld, ii
-
-
 def _check_variance_v2(M_annot, ref_ld):
     ii = ref_ld.var() == 0
     if ii.all():
@@ -247,31 +199,3 @@ def _read_w_ld(w_file):
     w_ld.columns = ["SNP", "LD_weights"]
 
     return w_ld
-
-
-# Fun for merging
-def _merge_and_log(ld, sumstats, noun):
-    """
-    Wrap smart merge with log messages about # of SNPs.
-    """
-    sumstats = smart_merge(ld, sumstats)
-    msg = "After merging with {F}, {N} SNPs remain."
-    if len(sumstats) == 0:
-        raise ValueError(msg.format(N=len(sumstats), F=noun))
-    else:
-        print(msg.format(N=len(sumstats), F=noun))
-    # -
-    return sumstats
-
-
-def smart_merge(x, y):
-    """
-    Check if SNP columns are equal. If so, save time by using concat instead of merge.
-    """
-    if len(x) == len(y) and (x.index == y.index).all() and (x.SNP == y.SNP).all():
-        x = x.reset_index(drop=True)
-        y = y.reset_index(drop=True).drop("SNP", 1)
-        out = pd.concat([x, y], axis=1)
-    else:
-        out = pd.merge(x, y, how="inner", on="SNP")
-    return out

gsmap-1.73.0.dist-info/METADATA

@@ -0,0 +1,169 @@
+Metadata-Version: 2.4
+Name: gsMap
+Version: 1.73.0
+Summary: Genetics-informed pathogenic spatial mapping
+Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: POSIX :: Linux
+License-File: LICENSE
+Requires-Dist: numpy < 2.0.0
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: tqdm
+Requires-Dist: pyyaml
+Requires-Dist: torch
+Requires-Dist: torch-geometric
+Requires-Dist: pyranges
+Requires-Dist: pyfiglet
+Requires-Dist: plotly
+Requires-Dist: kaleido
+Requires-Dist: jinja2
+Requires-Dist: scanpy >=1.8.0
+Requires-Dist: zarr>=2,<3
+Requires-Dist: bitarray >=2.9.2, <3.0.0
+Requires-Dist: pyarrow
+Requires-Dist: scikit-misc
+Requires-Dist: sphinx ; extra == "doc"
+Requires-Dist: sphinx-argparse ; extra == "doc"
+Requires-Dist: sphinx-autobuild ; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
+Requires-Dist: sphinx-basic-ng ; extra == "doc"
+Requires-Dist: sphinx-charts ; extra == "doc"
+Requires-Dist: sphinx-copybutton ; extra == "doc"
+Requires-Dist: sphinx_inline_tabs ; extra == "doc"
+Requires-Dist: sphinx-markdown-tables ; extra == "doc"
+Requires-Dist: sphinx-rtd-theme ; extra == "doc"
+Requires-Dist: sphinxcontrib-applehelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-devhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-htmlhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-jquery ; extra == "doc"
+Requires-Dist: sphinxcontrib-jsmath ; extra == "doc"
+Requires-Dist: sphinxcontrib-qthelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
+Requires-Dist: furo ; extra == "doc"
+Requires-Dist: myst-parser ; extra == "doc"
+Requires-Dist: nbsphinx ; extra == "doc"
+Requires-Dist: pytest>=7.0.0 ; extra == "tests"
+Requires-Dist: pytest-cov>=4.0.0 ; extra == "tests"
+Requires-Dist: coverage ; extra == "tests"
+Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
+Project-URL: Home, https://github.com/JianYang-Lab/gsMap
+Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
+Provides-Extra: doc
+Provides-Extra: tests
+
+# gsMap
+
+|               |                                                                                                      |                |                                                                                                    |
+| ------------- | ---------------------------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------- |
+| __Version__   | [![PyPI version][pypi-badge]][pypi-url] [![Python][python-badge]][python-url]                        | __Status__     | [![Project Status][status-badge]][status-url] [![Maintenance][maintenance-badge]][maintenance-url] |
+| __Activity__  | [![GitHub commits][commits-badge]][commits-url] [![Last Commit][last-commit-badge]][last-commit-url] | __Quality__    | [![codecov][codecov-badge]][codecov-url] [![Ruff][ruff-badge]][ruff-url]                           |
+| __CI/CD__     | [![Docs][docs-badge]][docs-url] [![test][test-badge]][test-url]                                      | __Community__  | [![GitHub stars][stars-badge]][stars-url] [![GitHub forks][forks-badge]][forks-url]                |
+| __Downloads__ | [![Downloads][downloads-badge]][downloads-url]                                                       | __License__    | [![License: MIT][license-badge]][license-url] [![DOI][doi-badge]][doi-url]                         |
+| __Platform__  | [![Linux][linux-badge]][linux-url]                                                                   | __Contribute__ | [![Issues][issues-badge]][issues-url] [![PRs Welcome][pr-badge]][pr-url]                           |
+
+## Introduction
+
+`gsMap` (genetically informed spatial mapping of cells for complex traits)
+integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
+summary statistics to map cells to human complex traits, including diseases,
+in a spatially resolved manner.
+
+## Key Features
+
+- __Spatially-aware High-Resolution Trait Mapping__
+- __Spatial Region Identification__
+- __Putative Causal Genes Identification__
+
+![Model Architecture](schematic.png)
+
+## Installation
+
+Install using pip:
+
+```bash
+conda create -n gsMap python>=3.10
+conda activate gsMap
+pip install gsMap
+```
+
+Install from source:
+
+```bash
+git clone https://github.com/JianYang-Lab/gsMap
+cd gsMap
+pip install -e .
+```
+
+Verify the installation by running the following command:
+
+```bash
+gsmap --help
+```
+
+## Usage
+
+Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
+
+## Online Visualization
+
+To visualize the traits-cell association spatial maps,
+please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
+
+## Citation
+
+Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
+[Spatially resolved mapping of cells associated with human complex traits.](https://doi.org/10.1038/s41586-025-08757-x)
+Nature (2025).
+
+Please cite the paper and give us a STAR if you find gsMap useful for your research.
+
+<!-- Badge links -->
+
+[codecov-badge]: https://codecov.io/gh/JianYang-Lab/gsMap/graph/badge.svg?token=NFZFXZIEUU
+[codecov-url]: https://codecov.io/gh/JianYang-Lab/gsMap
+[commits-badge]: https://img.shields.io/github/commit-activity/m/JianYang-Lab/gsMap
+[commits-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[docs-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml/badge.svg
+[docs-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml
+[doi-badge]: https://img.shields.io/badge/DOI-10.1038%2Fs41586--025--08757--x-blue
+[doi-url]: https://doi.org/10.1038/s41586-025-08757-x
+[downloads-badge]: https://static.pepy.tech/badge/gsMap
+[downloads-url]: https://pepy.tech/project/gsMap
+[forks-badge]: https://img.shields.io/github/forks/JianYang-Lab/gsMap
+[forks-url]: https://github.com/JianYang-Lab/gsMap/network/members
+[issues-badge]: https://img.shields.io/github/issues/JianYang-Lab/gsMap
+[issues-url]: https://github.com/JianYang-Lab/gsMap/issues
+[last-commit-badge]: https://img.shields.io/github/last-commit/JianYang-Lab/gsMap
+[last-commit-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
+[license-url]: https://opensource.org/licenses/MIT
+[linux-badge]: https://img.shields.io/badge/Linux-%E2%9C%93-success
+[linux-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
+[maintenance-badge]: https://img.shields.io/badge/Maintained%3F-yes-green.svg
+[maintenance-url]: https://github.com/JianYang-Lab/gsMap/graphs/commit-activity
+[pr-badge]: https://img.shields.io/badge/PRs-welcome-brightgreen.svg
+[pr-url]: https://github.com/JianYang-Lab/gsMap/pulls
+[pypi-badge]: https://img.shields.io/pypi/v/gsMap
+[pypi-url]: https://pypi.org/project/gsMap/
+[python-badge]: https://img.shields.io/pypi/pyversions/gsMap
+[python-url]: https://www.python.org
+[ruff-badge]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+[ruff-url]: https://github.com/astral-sh/ruff
+[stars-badge]: https://img.shields.io/github/stars/JianYang-Lab/gsMap
+[stars-url]: https://github.com/JianYang-Lab/gsMap/stargazers
+[status-badge]: https://www.repostatus.org/badges/latest/active.svg
+[status-url]: https://www.repostatus.org/#active
+[test-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml/badge.svg
+[test-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
+

gsmap-1.73.0.dist-info/RECORD

@@ -0,0 +1,31 @@
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+gsMap/__main__.py,sha256=Vdhw8YA1K3wPMlbJQYL5WqvRzAKVeZ16mZQFO9VRmCo,62
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+gsMap/config.py,sha256=QaDM3Um6p3rcQO-HTMts8-mQ85RmPCJ2RK2kjC32Bgg,51246
+gsMap/create_slice_mean.py,sha256=bkobWq1kPSvVUZb5RUxYR6ckGGmsftVYCcHfU4xpT6w,5676
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+gsMap/latent_to_gene.py,sha256=CqvlH2qriuzWTt-hjfzgMD1VEd4PNSSG4A4ODvSbUfA,12398
+gsMap/main.py,sha256=SzfAXhrlr4LXnSD4gkvAtUUPYXyra6a_MzVCxDBZjr0,1170
+gsMap/report.py,sha256=_1FYkzGhVGMnvHgEQ8z51iMrVEVlh48a31jLqbV2o9w,6953
+gsMap/run_all_mode.py,sha256=0fJWV6TL7o2OAUXyhC0okHav6gydVUXOinP-HJ-DaAQ,9325
+gsMap/setup.py,sha256=lsIQCChHwR0ojWZs7xay8rukRaLlueuLkc83bp-B2ZE,103
+gsMap/spatial_ldsc_multiple_sumstats.py,sha256=-mawOBjn8-Y5Irl8mv8ye83hfiEJ1mkLrRIQiI-XaMM,17973
+gsMap/visualize.py,sha256=N55s-xmzSd_DtIesrGewfDeoytYUcMd2acDsjEpChCA,7242
+gsMap/GNN/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gsMap/GNN/adjacency_matrix.py,sha256=MfkhgpAHJcC-3l_iZDQQYD30w4bpe29-8s6kkGxiwQw,3231
+gsMap/GNN/model.py,sha256=75In9sxBkaqqpCQSrQEUO-zsQQVQnkXVbKsAgyAZjiQ,2918
+gsMap/GNN/train.py,sha256=S6s-AufN9GJNcgC5Mqe6MjcJAsaNnbDlHUoYHcvxFmA,3069
+gsMap/templates/report_template.html,sha256=QODZEbVxpW1xsLz7lDrD_DyUfzYoi9E17o2tLJlf8OQ,8016
+gsMap/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+gsMap/utils/generate_r2_matrix.py,sha256=Hwp70pQfMoWjvDa8LyrtZsvws3YHKj5oGYB_LB2CSqs,17293
+gsMap/utils/jackknife.py,sha256=w_qMj9GlqViouHuOw1U80N6doWuCTXuPoAVU4P-5mm8,17673
+gsMap/utils/manhattan_plot.py,sha256=N7jd0Cn-7JMsTBgv41k1w0174rqnPT-v7xLIV2cfY5U,25241
+gsMap/utils/regression_read.py,sha256=rKA0nkUpTJf6WuGddhKrsBCExchDNEyojOWu_qddZNw,5474
+gsmap-1.73.0.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
+gsmap-1.73.0.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
+gsmap-1.73.0.dist-info/WHEEL,sha256=_2ozNFCLWc93bK4WKHCO-eDUENDlo-dgc9cU3qokYO4,82
+gsmap-1.73.0.dist-info/METADATA,sha256=Z6rfdCCrlRN1_DRzoIhCwshs9b94LDJVwHNYRLF5bko,8075
+gsmap-1.73.0.dist-info/RECORD,,

{gsmap-1.72.3.dist-info → gsmap-1.73.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: flit 3.10.1
+Generator: flit 3.11.0
 Root-Is-Purelib: true
 Tag: py3-none-any

{gsmap-1.72.3.dist-info → gsmap-1.73.0.dist-info/licenses}/LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) 2023 liyang
+Copyright (c) 2025 JianYang-Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -9,13 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.