gsMap 1.73.2__py3-none-any.whl → 1.73.3__py3-none-any.whl

gsMap/__init__.py

@@ -2,4 +2,4 @@
 Genetics-informed pathogenic spatial mapping
 """
 
-__version__ = "1.73.2"
+__version__ = "1.73.3"

gsMap/generate_ldscore.py

@@ -57,7 +57,8 @@ def load_gtf(
     gtf = gtf[gtf["Feature"] == "gene"]
 
     # Find common genes between GTF and marker scores
-    common_gene = np.intersect1d(mk_score.index, gtf.gene_name)
+    # common_gene = np.intersect1d(mk_score.index, gtf.gene_name)
+    common_gene = list(set(mk_score.index) & set(gtf.gene_name))
     logger.info(f"Found {len(common_gene)} common genes between GTF and marker scores")
 
     # Filter GTF and marker scores to common genes
@@ -69,6 +70,9 @@ def load_gtf(
 
     # Process the GTF (open window around gene coordinates)
     gtf_bed = gtf[["Chromosome", "Start", "End", "gene_name", "Strand"]].copy()
+    gtf_bed["Chromosome"] = gtf_bed["Chromosome"].apply(
+        lambda x: f"chr{x}" if not str(x).startswith("chr") else x
+    )
     gtf_bed.loc[:, "TSS"] = gtf_bed["Start"]
     gtf_bed.loc[:, "TED"] = gtf_bed["End"]
 
@@ -128,7 +132,7 @@ def load_bim(bfile_root: str, chrom: int) -> tuple[pd.DataFrame, pr.PyRanges]:
         - bim_pr is a PyRanges object with BIM data
     """
     bim_file = f"{bfile_root}.{chrom}.bim"
-    logger.debug(f"Loading BIM file: {bim_file}")
+    logger.info(f"Loading BIM file: {bim_file}")
 
     bim = pd.read_csv(bim_file, sep="\t", header=None)
     bim.columns = ["CHR", "SNP", "CM", "BP", "A1", "A2"]
@@ -311,6 +315,8 @@ def get_ldscore(
         bfile_chr_prefix=f"{bfile_root}.{chrom}", keep_snps=keep_snps_index
     )
 
+    annot_matrix = annot_matrix[geno_array.kept_snps, :]
+
     # Configure LD window based on specified unit
     if ld_unit == "SNP":
         max_dist = ld_wind

{gsmap-1.73.2.dist-info → gsmap-1.73.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gsMap
-Version: 1.73.2
+Version: 1.73.3
 Summary: Genetics-informed pathogenic spatial mapping
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.10

{gsmap-1.73.2.dist-info → gsmap-1.73.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-gsMap/__init__.py,sha256=xjO1mrd3lI32sCY5mQ8rHHD4yyTbUr94E758a72nT4c,77
+gsMap/__init__.py,sha256=0XtiYZAbXor3EAyHAebfh1qGJuKOgeB3h1MPE6ukNNY,77
 gsMap/__main__.py,sha256=Vdhw8YA1K3wPMlbJQYL5WqvRzAKVeZ16mZQFO9VRmCo,62
 gsMap/cauchy_combination_test.py,sha256=SiUyqJKr4ATFtRgsCEJ43joGcSagCOnnurkB1FlQiB4,5105
 gsMap/config.py,sha256=LmBVMb0eda6bfrKkQuh7eZnZdvgecjCnozRd_clqvlY,51584
@@ -6,7 +6,7 @@ gsMap/create_slice_mean.py,sha256=Nnmb7ACtS-9TurW5xQ4TqCinejPsYcvuT5Oxqa5Uges,57
 gsMap/diagnosis.py,sha256=YyT_TkPbb3c22DLpRYu9yynbNGrhytcCgxCoPwz9Bpc,12962
 gsMap/find_latent_representation.py,sha256=aZ5fFY2RhAsNaDeoehd5lN28556d6GGHK9xEUTvo6G4,5365
 gsMap/format_sumstats.py,sha256=1c9OgbqDQWOgXeSrbAhbJfChv_2IwXIgLE6Pbw2sx0s,13778
-gsMap/generate_ldscore.py,sha256=xxzbaANl638bRvRAowrTPmFA4dEC0zDBv6i8KQTJvJ8,45094
+gsMap/generate_ldscore.py,sha256=G108fVVdGj0Pn50TqFmAXLjQ7OTY9BWnilHoDeIn2D8,45348
 gsMap/latent_to_gene.py,sha256=sDPvOU4iF-HkfQY0nnkIVXpjyTQ9-PjQflwEFWrPg-A,12869
 gsMap/main.py,sha256=SzfAXhrlr4LXnSD4gkvAtUUPYXyra6a_MzVCxDBZjr0,1170
 gsMap/report.py,sha256=_1FYkzGhVGMnvHgEQ8z51iMrVEVlh48a31jLqbV2o9w,6953
@@ -24,8 +24,8 @@ gsMap/utils/generate_r2_matrix.py,sha256=0zyoJDWUVavlQtR6_XXb7Ah9UhPyT3n0t6XCqlI
 gsMap/utils/jackknife.py,sha256=w_qMj9GlqViouHuOw1U80N6doWuCTXuPoAVU4P-5mm8,17673
 gsMap/utils/manhattan_plot.py,sha256=4ok5CHAaT_MadyMPnFZMR_llmE8Vf4-KiEfametgHq0,25480
 gsMap/utils/regression_read.py,sha256=rKA0nkUpTJf6WuGddhKrsBCExchDNEyojOWu_qddZNw,5474
-gsmap-1.73.2.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
-gsmap-1.73.2.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
-gsmap-1.73.2.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-gsmap-1.73.2.dist-info/METADATA,sha256=giDX_EkW5AutmnHHukvC2Kw29fY-q939rA9cWJP5pMY,8196
-gsmap-1.73.2.dist-info/RECORD,,
+gsmap-1.73.3.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
+gsmap-1.73.3.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
+gsmap-1.73.3.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+gsmap-1.73.3.dist-info/METADATA,sha256=-MD9qe4n_qOVF1dAQ6gcSLtCl1DZDMeoRw2EVijGDms,8196
+gsmap-1.73.3.dist-info/RECORD,,