gwaslab 3.4.44__py3-none-any.whl → 3.4.45__py3-none-any.whl

gwaslab/g_SumstatsPair.py

@@ -139,7 +139,7 @@ class SumstatsPair( ):
         self.clumps["clumps"], self.clumps["plink_log"] = _clump(self.data, log=self.log, p="P_1",mlog10p="MLOG10P_1", study = self.study_name, **kwargs)
 
     def to_coloc(self,**kwargs):
-        self.to_finemapping_file_path, self.plink_log = tofinemapping(self.data,study=self.study_name,suffixes=self.suffixes,log=self.log,**kwargs)
+        self.to_finemapping_file_path, output_file_list, self.plink_log = tofinemapping(self.data,study=self.study_name,suffixes=self.suffixes,log=self.log,**kwargs)
 
     def run_coloc_susie(self,**kwargs):
 

gwaslab/g_vchange_status.py

@@ -1,13 +1,15 @@
 import pandas as pd
 
+CATEGORIES = {str(j+i) for j in [1900000,3800000,9700000,9800000,9900000] for i in range(0,100000)}
+
 def vchange_status(status,digit,before,after):
     dic={}
     for i in range(len(before)):
         dic[before[i]]=after[i]
     if digit>1:
-        return status.str[:digit-1]+status.str[digit-1].replace(dic)+status.str[digit:]
+        return pd.Categorical(status.str[:digit-1]+status.str[digit-1].replace(dic)+status.str[digit:],categories=CATEGORIES)
     else:
-        return status.str[digit-1].replace(dic)+status.str[digit:]
+        return pd.Categorical(status.str[digit-1].replace(dic)+status.str[digit:],categories=CATEGORIES)
 
 def copy_status(from_status,to_status, digit):
     if digit>1:

gwaslab/g_version.py

@@ -15,8 +15,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.4.44",
-   "release_date":"20240424"
+   "version":"3.4.45",
+   "release_date":"20240509"
     }
     return dic   
 

gwaslab/hm_harmonize_sumstats.py

@@ -355,7 +355,11 @@ def oldcheckref(sumstats,ref_seq,chrom="CHR",pos="POS",ea="EA",nea="NEA",status=
     
     log.write("\n",end="",show_time=False,verbose=verbose) 
         
-    sumstats[status] = sumstats[status].astype("string")
+    CATEGORIES = {str(j+i) for j in [1900000,3800000,9700000,9800000,9900000] for i in range(0,100000)}
+    sumstats[status] = pd.Categorical(sumstats[status],categories=CATEGORIES)
+    #sumstats[status] = sumstats[status].astype("string")
+
+
     available_to_check =sum( (~sumstats[pos].isna()) & (~sumstats[nea].isna()) & (~sumstats[ea].isna()))
     status_0=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[0]\w", case=False, flags=0, na=False))
     status_3=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[3]\w", case=False, flags=0, na=False))
@@ -669,9 +673,11 @@ def checkref(sumstats,ref_seq,chrom="CHR",pos="POS",ea="EA",nea="NEA",status="ST
         sumstats_to_check = sumstats.loc[to_check_ref,[chrom,pos,ea,nea,status]]
         sumstats.loc[to_check_ref,status] = check_status(sumstats_to_check, all_records_dict, log=log, verbose=verbose)
         log.write(" -Finished checking records", verbose=verbose) 
- 
-    sumstats[status] = sumstats[status].astype("string")
-        
+    
+    CATEGORIES = {str(j+i) for j in [1900000,3800000,9700000,9800000,9900000] for i in range(0,100000)}
+    sumstats[status] = pd.Categorical(sumstats[status],categories=CATEGORIES)
+    #sumstats[status] = sumstats[status].astype("string")
+
     available_to_check =sum( (~sumstats[pos].isna()) & (~sumstats[nea].isna()) & (~sumstats[ea].isna()))
     status_0=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[0]\w", case=False, flags=0, na=False))
     status_3=sum(sumstats["STATUS"].str.match("\w\w\w\w\w[3]\w", case=False, flags=0, na=False))
@@ -700,6 +706,7 @@ def checkref(sumstats,ref_seq,chrom="CHR",pos="POS",ea="EA",nea="NEA",status="ST
     if remove is True:
         sumstats = sumstats.loc[~sumstats["STATUS"].str.match("\w\w\w\w\w[8]\w"),:]
         log.write(" -Variants not on given reference sequence were removed.",verbose=verbose)
+
     
     finished(log, verbose, _end_line)
     return sumstats

{gwaslab-3.4.44.dist-info → gwaslab-3.4.45.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.44
+Version: 3.4.45
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -8,7 +8,7 @@ Project-URL: Github, https://github.com/Cloufield/gwaslab
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: <=3.10,>=3.9
+Requires-Python: <3.11,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: LICENSE_before_v3.4.39
@@ -17,7 +17,7 @@ Requires-Dist: numpy >=1.21.2
 Requires-Dist: matplotlib !=3.7.2,>=3.5
 Requires-Dist: seaborn >=0.12
 Requires-Dist: scipy >=1.12
-Requires-Dist: pySAM <0.20,>=0.18.1
+Requires-Dist: pySAM ==0.22.1
 Requires-Dist: Biopython >=1.79
 Requires-Dist: adjustText <=0.8,>=0.7.3
 Requires-Dist: liftover >=1.1.13

{gwaslab-3.4.44.dist-info → gwaslab-3.4.45.dist-info}/RECORD

@@ -7,14 +7,14 @@ gwaslab/cache_manager.py,sha256=HOTnSkCOyGEPLRl90WT8D_6pAdI8d8AzenMIDGuCeWc,2811
 gwaslab/g_Log.py,sha256=C3Zv-_6c3C9ms8bgQ-ytplz22sjk7euqXYkWr9zNeAs,1573
 gwaslab/g_Phenotypes.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gwaslab/g_Sumstats.py,sha256=NOEQd00guGch_GIt5bHv1wcrAvETfChqzmtgm-nIx_I,35298
-gwaslab/g_SumstatsPair.py,sha256=tbgT-_1CqDEw22s4LbVJWF3ChELxz0gy1DEBzLc9ODU,8833
+gwaslab/g_SumstatsPair.py,sha256=20snPb4SlI6ftMGVjgxAuyxsxYRQF-GzzlBSnoB-3Lo,8851
 gwaslab/g_SumstatsT.py,sha256=u_DighLMnMxwTLnqm-B58pA0G6WXRj6pudPyKMVKjSU,2133
 gwaslab/g_Sumstats_summary.py,sha256=FECvvFXJVKaCX5dggBvvk9YvJ6AbdbcLfjltysX7wEE,6380
 gwaslab/g_meta.py,sha256=htWlgURWclm9R6UqFcX1a93WN27xny7lGUeyJZOtszQ,2583
-gwaslab/g_vchange_status.py,sha256=eX0jdIb6Spa07ZdpWNqUWqdVBWS0fuH2yrt4PDi3Res,1746
-gwaslab/g_version.py,sha256=44qNMttuGuAyDPPblc1z0V9R5lHo9z8x2_E6JuZ6eBE,1818
+gwaslab/g_vchange_status.py,sha256=jLoVzMJFhB5k_cJKzHuBNc2HZGBWydAunCNa0n_d54g,1923
+gwaslab/g_version.py,sha256=49_gR8lEQ_jgmfO9XJszEzuzDIESj5dHj6gta3Ilkmw,1818
 gwaslab/hm_casting.py,sha256=FqP4EQl83Q2OKLw004OgLIvUH795TVCGwziLk5jsHqY,11368
-gwaslab/hm_harmonize_sumstats.py,sha256=CADIG_KLsoq4y21wN0fyaaG2S4PDpKu96Y0of6b0TaU,78184
+gwaslab/hm_harmonize_sumstats.py,sha256=ympk2MZkbb0MnZ1n2ajkV36L8EAm7nBEaYhjqjI38tU,78548
 gwaslab/hm_rsid_to_chrpos.py,sha256=ODWREO0jPN0RAfNzL5fRzSRANfhiksOvUVPuEsFZQqA,6552
 gwaslab/io_preformat_input.py,sha256=w62JLAr16Ru0EgUtBCEV2eXRO89OqhidQxwf2IPAM38,20014
 gwaslab/io_read_ldsc.py,sha256=8S9n4imgl4d0WPms_GYld-6uUM5z7iWGiCA-M814kzY,12123
@@ -73,9 +73,9 @@ gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz,sha256=qD9RsC5S2h6l-OdpW
 gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz,sha256=Y8ZT2FIAhbhlgCJdE9qQVAiwnV_fcsPt72usBa7RSBM,10225828
 gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz,sha256=R7IkssKu0L4WwkU9SrS84xCMdrkkKL0gnTNO_OKbG0Y,219
 gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz,sha256=76CIU0pibDJ72Y6UY-TbIKE9gEPwTELAaIbCXyjm80Q,470
-gwaslab-3.4.44.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gwaslab-3.4.44.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
-gwaslab-3.4.44.dist-info/METADATA,sha256=PJUO56s9S_nfVnZlRCYuSq-6BADrRxjcwjAqaAjJWc8,7764
-gwaslab-3.4.44.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-gwaslab-3.4.44.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
-gwaslab-3.4.44.dist-info/RECORD,,
+gwaslab-3.4.45.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gwaslab-3.4.45.dist-info/LICENSE_before_v3.4.39,sha256=GhLOU_1UDEKeOacYhsRN_m9u-eIuVTazSndZPeNcTZA,1066
+gwaslab-3.4.45.dist-info/METADATA,sha256=5FN5dbVypNPET635Eooi01_1NDFD1dNr1T9Jv0JXmLc,7757
+gwaslab-3.4.45.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+gwaslab-3.4.45.dist-info/top_level.txt,sha256=PyY6hWtrALpv2MAN3kjkIAzJNmmBTH5a2risz9KwH08,8
+gwaslab-3.4.45.dist-info/RECORD,,