deleted format function

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## [0.2.2] - 2023-03-22
+
+### Added
+
+
+### Changed
+- deleted format function
+
+
+### Fixed
+
+
 ## [0.2.1] - 2023-01-10
 
 ### Added

easyfinemap/cli.py

@@ -77,28 +77,28 @@ def validate_ldref(
     ld.valid(ldref_path, outprefix, file_type, mac, threads)
 
 
-@app.command()
-def validate_sumstats(
-    sumstats_path: Path = typer.Argument(..., help="The path to the GWAS summary statistics file."),
-    output: Path = typer.Argument(..., help="The output prefix."),
-) -> None:
-    """Validate the GWAS summary statistics file."""
-    if sumstats_path.exists():
-        sumstats = pd.read_csv(sumstats_path, sep="\t")
-        typer.echo(f"Loaded {sumstats_path} successfully.")
-        typer.echo(f"Number of SNPs: {sumstats.shape[0]}")
-        typer.echo(f"Number of columns: {sumstats.shape[1]}")
-        typer.echo(f"Columns: {list(sumstats.columns)}")
-        valid_sumstats = SumStat(sumstats)
-        valid_sumstats = valid_sumstats.standarize()
-        if output.suffix == ".gz":
-            valid_sumstats.to_csv(output, sep="\t", index=False, compression="gzip")
-        else:
-            valid_sumstats.to_csv(output, sep="\t", index=False)
-        typer.echo(f"Saved the validated summary statistics to {output}.")
-    else:
-        logging.error(f"No such file of {sumstats_path}.")
-        sys.exit(1)
+# @app.command()
+# def validate_sumstats(
+#     sumstats_path: Path = typer.Argument(..., help="The path to the GWAS summary statistics file."),
+#     output: Path = typer.Argument(..., help="The output prefix."),
+# ) -> None:
+#     """Validate the GWAS summary statistics file."""
+#     if sumstats_path.exists():
+#         sumstats = pd.read_csv(sumstats_path, sep="\t")
+#         typer.echo(f"Loaded {sumstats_path} successfully.")
+#         typer.echo(f"Number of SNPs: {sumstats.shape[0]}")
+#         typer.echo(f"Number of columns: {sumstats.shape[1]}")
+#         typer.echo(f"Columns: {list(sumstats.columns)}")
+#         valid_sumstats = SumStat(sumstats)
+#         valid_sumstats = valid_sumstats.standarize()
+#         if output.suffix == ".gz":
+#             valid_sumstats.to_csv(output, sep="\t", index=False, compression="gzip")
+#         else:
+#             valid_sumstats.to_csv(output, sep="\t", index=False)
+#         typer.echo(f"Saved the validated summary statistics to {output}.")
+#     else:
+#         logging.error(f"No such file of {sumstats_path}.")
+#         sys.exit(1)
 
 
 @app.command()

easyfinemap/easyfinemap.py

@@ -30,7 +30,7 @@
 from easyfinemap.ldref import LDRef
 from easyfinemap.sumstat import SumStat
 from easyfinemap.tools import Tools
-from easyfinemap.utils import io_in_tempdir
+from easyfinemap.utils import io_in_tempdir, make_SNPID_unique
 
 
 class EasyFinemap(object):
@@ -581,8 +581,7 @@ def finemap_all_loci(
         threads : int, optional
             Number of threads, by default 1
         """
-        sumstats = SumStat(sumstats)
-        sumstats = sumstats.standarize()
+        sumstats = make_SNPID_unique(sumstats)
         if credible_threshold and credible_method is None and methods != ["all"] and len(methods) == 1:
             credible_method = methods[0]
         kwargs_list = []

easyfinemap/loci.py

@@ -22,7 +22,7 @@
 from easyfinemap.ldref import LDRef
 from easyfinemap.sumstat import SumStat
 from easyfinemap.tools import Tools
-from easyfinemap.utils import get_significant_snps, io_in_tempdir
+from easyfinemap.utils import get_significant_snps, io_in_tempdir, make_SNPID_unique
 
 
 class Loci:
@@ -101,8 +101,7 @@ def identify_indep_loci(
         Tuple[pd.DataFrame, pd.DataFrame]
             The independent lead snps and independent loci.
         """
-        sumstats = SumStat(sumstats)
-        sumstats = sumstats.standarize()
+        sumstats = make_SNPID_unique(sumstats)
         if method == "distance":
             sig_df = get_significant_snps(sumstats, sig_threshold)
             lead_snp = self.indep_snps_by_distance(sig_df, distance)