gsMap 1.73.4__py3-none-any.whl → 1.73.5__py3-none-any.whl

gsMap/__init__.py

@@ -1,5 +1,5 @@
 """
-Genetics-informed pathogenic spatial mapping
+Genetically informed spatial mapping of cells for complex traits
 """
 
-__version__ = "1.73.4"
+__version__ = "1.73.5"

gsMap/utils/generate_r2_matrix.py

@@ -94,26 +94,26 @@ class PlinkBEDFile:
         # Filter out invalid SNPs
         valid_mask = self.all_snp_info["valid_snp"]
         if num_invalid := np.sum(~valid_mask):
-            logger.warning(f"Filtering out {num_invalid} bad quality SNPs")
+            logger.warning(
+                f"Filtering out {num_invalid} bad quality SNPs: {self.bim_df.loc[~valid_mask, 'SNP'].tolist()}"
+            )
         else:
             logger.info("All SNPs passed the basic quality check")
 
-        # Only keep valid SNPs
-        self.kept_snps = np.arange(self.m_original)[valid_mask]
-
-        # Update bim_df to only include valid SNPs and reset index
-        self.bim_df = self.bim_df.loc[valid_mask].reset_index(drop=True)
-
         # Create new genotype data with only the valid SNPs
         new_geno = ba.bitarray()
-        for j in self.kept_snps:
+        for j in np.arange(self.m_original)[valid_mask]:
             new_geno += self.geno_original[
                 2 * self.nru_original * j : 2 * self.nru_original * (j + 1)
             ]
 
         # Update original data to only include valid SNPs
         self.geno_original = new_geno
-        self.m_original = len(self.kept_snps)
+
+        # Only keep valid SNPs
+        self.bim_df = self.bim_df.loc[valid_mask].reset_index(drop=True)
+        self.m_original = len(self.bim_df)
+        self.kept_snps = np.arange(self.m_original)
 
         # Initialize current state variables
         self._currentSNP = 0
@@ -292,8 +292,8 @@ class PlinkBEDFile:
 
         # Apply MAF filter using pre-calculated values
         if mafMin is not None and mafMin > 0:
-            maf_values = np.minimum(self.all_snp_info["freq"], 1 - self.all_snp_info["freq"])
-            maf_mask = (maf_values > mafMin) & self.all_snp_info["valid_snp"]
+            # Remove the redundant valid_snp check since all SNPs are already valid
+            maf_mask = self.maf > mafMin
             kept_snps = kept_snps[maf_mask]
             logger.info(f"After MAF filtering (>{mafMin}), {len(kept_snps)} SNPs remain")
 
@@ -369,9 +369,7 @@ class PlinkBEDFile:
         list
             List of SNP IDs that pass the MAF threshold
         """
-        # Use the pre-calculated MAF values
-        maf_values = np.minimum(self.all_snp_info["freq"], 1 - self.all_snp_info["freq"])
-        maf_mask = (maf_values > mafMin) & self.all_snp_info["valid_snp"]
+        maf_mask = self.maf > mafMin
 
         # Get SNP names from the BIM dataframe
         snp_pass_maf = self.bim_df.loc[maf_mask, "SNP"].tolist()

{gsmap-1.73.4.dist-info → gsmap-1.73.5.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: gsMap
-Version: 1.73.4
-Summary: Genetics-informed pathogenic spatial mapping
+Version: 1.73.5
+Summary: Genetically informed spatial mapping of cells for complex traits
 Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{gsmap-1.73.4.dist-info → gsmap-1.73.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-gsMap/__init__.py,sha256=hRDqmAAKm9MYDtkkkVvoAJQDZAlG2yZ5nafywVU2Ufo,77
+gsMap/__init__.py,sha256=ra0VGxzGpetF2e7p415XeprzKQVQSon_5Gv_DnlbYHU,97
 gsMap/__main__.py,sha256=Vdhw8YA1K3wPMlbJQYL5WqvRzAKVeZ16mZQFO9VRmCo,62
 gsMap/cauchy_combination_test.py,sha256=SiUyqJKr4ATFtRgsCEJ43joGcSagCOnnurkB1FlQiB4,5105
 gsMap/config.py,sha256=xQQJKqe-ZLohxzEZ0L_CEXXbbUK-U6-H6BnISteqrHs,51316
@@ -20,12 +20,12 @@ gsMap/GNN/model.py,sha256=75In9sxBkaqqpCQSrQEUO-zsQQVQnkXVbKsAgyAZjiQ,2918
 gsMap/GNN/train.py,sha256=4qipaxaz3rQOtlRpTYCfl1Oz4kz_A6vNB1aw8_gGK_k,3076
 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=0FEbSEiZhNj3nnnt9V-fp7WWPLpfBci3tP4ydBbG280,20114
+gsMap/utils/generate_r2_matrix.py,sha256=5LX99x7k404NyV52CmegdZi9Pm9nh5X2JElisdN2PU0,19915
 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=uBSKlvYVhUKmDSCBvKHQrE1wLNyvK-rbzc5TJV51oDI,5649
-gsmap-1.73.4.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
-gsmap-1.73.4.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
-gsmap-1.73.4.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
-gsmap-1.73.4.dist-info/METADATA,sha256=fyLpDSS5SEIyPj9rZ7ymcXPIOCLcAU2j-OW0D5xC2GA,8196
-gsmap-1.73.4.dist-info/RECORD,,
+gsmap-1.73.5.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
+gsmap-1.73.5.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
+gsmap-1.73.5.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+gsmap-1.73.5.dist-info/METADATA,sha256=9a7ejINVfz1GXHCAm959bnjFYJcQDmS9upYe1ISIkHU,8216
+gsmap-1.73.5.dist-info/RECORD,,