gwaslab 3.5.5__py3-none-any.whl → 3.5.6__py3-none-any.whl

gwaslab/g_SumstatsSet.py

@@ -0,0 +1,663 @@
+import pandas as pd
+import numpy as np
+import time
+import re
+import copy
+from gwaslab.g_Sumstats_summary import summarize
+from gwaslab.g_Sumstats_summary import lookupstatus
+from gwaslab.io_preformat_input import preformat
+from gwaslab.io_to_formats import _to_format
+from gwaslab.g_Log import Log
+from gwaslab.qc_fix_sumstats import fixID
+from gwaslab.qc_fix_sumstats import flipSNPID
+from gwaslab.qc_fix_sumstats import stripSNPID
+from gwaslab.qc_fix_sumstats import removedup
+from gwaslab.qc_fix_sumstats import fixchr
+from gwaslab.qc_fix_sumstats import fixpos
+from gwaslab.qc_fix_sumstats import fixallele
+from gwaslab.qc_fix_sumstats import parallelnormalizeallele
+from gwaslab.qc_fix_sumstats import sanitycheckstats
+from gwaslab.qc_fix_sumstats import parallelizeliftovervariant
+from gwaslab.qc_fix_sumstats import flipallelestats
+from gwaslab.qc_fix_sumstats import sortcoordinate
+from gwaslab.qc_fix_sumstats import sortcolumn
+from gwaslab.qc_fix_sumstats import _set_build
+from gwaslab.qc_fix_sumstats import _process_build
+from gwaslab.hm_harmonize_sumstats import parallelecheckaf
+from gwaslab.hm_harmonize_sumstats import paralleleinferaf
+from gwaslab.hm_harmonize_sumstats import checkref
+from gwaslab.hm_harmonize_sumstats import oldcheckref
+from gwaslab.hm_harmonize_sumstats import rsidtochrpos
+from gwaslab.hm_harmonize_sumstats import parallelizeassignrsid
+from gwaslab.hm_harmonize_sumstats import parallelinferstrand
+from gwaslab.hm_harmonize_sumstats import parallelrsidtochrpos
+from gwaslab.hm_harmonize_sumstats import _paralleleinferafwithmaf
+from gwaslab.util_in_filter_value import filtervalues
+from gwaslab.util_in_filter_value import filterout
+from gwaslab.util_in_filter_value import filterin
+from gwaslab.util_in_filter_value import filterregionin
+from gwaslab.util_in_filter_value import filterregionout
+from gwaslab.util_in_filter_value import _filter_indel
+from gwaslab.util_in_filter_value import _filter_palindromic
+from gwaslab.util_in_filter_value import _filter_snp
+from gwaslab.util_in_filter_value import _exclude_hla
+from gwaslab.util_in_filter_value import inferbuild
+from gwaslab.util_in_filter_value import sampling
+from gwaslab.util_in_filter_value import _get_flanking
+from gwaslab.util_in_filter_value import _get_flanking_by_chrpos
+from gwaslab.util_in_filter_value import _get_flanking_by_id
+from gwaslab.util_in_calculate_gc import lambdaGC
+from gwaslab.util_in_convert_h2 import _get_per_snp_r2
+from gwaslab.util_in_get_sig import getsig
+from gwaslab.util_in_get_density import getsignaldensity
+from gwaslab.util_in_get_density import assigndensity
+from gwaslab.util_in_get_sig import annogene
+from gwaslab.util_in_get_sig import getnovel
+from gwaslab.util_in_get_sig import _check_cis
+from gwaslab.util_in_get_sig import _check_novel_set
+from gwaslab.util_in_fill_data import filldata
+from gwaslab.bd_get_hapmap3 import gethapmap3
+from gwaslab.bd_common_data import get_chr_list
+from gwaslab.bd_common_data import get_number_to_chr
+from gwaslab.bd_common_data import get_chr_to_number
+from gwaslab.bd_common_data import get_high_ld
+from gwaslab.bd_common_data import get_format_dict
+from gwaslab.bd_common_data import get_formats_list
+from gwaslab.g_version import _show_version
+from gwaslab.g_version import gwaslab_info
+from gwaslab.g_meta import _init_meta
+from gwaslab.g_meta import _append_meta_record
+from gwaslab.util_ex_run_clumping import _clump
+from gwaslab.util_ex_calculate_ldmatrix import tofinemapping
+from gwaslab.util_ex_calculate_prs import _calculate_prs
+from gwaslab.viz_plot_mqqplot import mqqplot
+from gwaslab.viz_plot_trumpetplot import plottrumpet
+from gwaslab.viz_plot_compare_af import plotdaf
+from gwaslab.util_ex_run_susie import _run_susie_rss
+from gwaslab.qc_fix_sumstats import _check_data_consistency
+from gwaslab.util_ex_ldsc import _estimate_h2_by_ldsc
+from gwaslab.util_ex_ldsc import _estimate_rg_by_ldsc
+from gwaslab.util_ex_ldsc import _estimate_h2_cts_by_ldsc
+from gwaslab.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
+from gwaslab.bd_get_hapmap3 import gethapmap3
+from gwaslab.util_abf_finemapping import abf_finemapping
+from gwaslab.util_abf_finemapping import make_cs
+from gwaslab.io_read_pipcs import _read_pipcs
+from gwaslab.viz_plot_credible_sets import _plot_cs
+import gc
+from gwaslab.viz_plot_phe_heatmap import _gwheatmap
+from gwaslab.viz_plot_effect import _plot_effect
+from gwaslab.util_in_merge import _extract_variant
+
+#20250215
+class SumstatsSet():
+    def __init__(self,
+             sumstats_dic,
+             variant_set=None,
+             build="99",
+             species="homo sapiens",
+             build_infer=False,
+             set="set1",
+             verbose=True,
+             **readargs):
+
+        # basic attributes
+        self.data = pd.DataFrame()
+        self.log = Log()
+        # meta information
+
+        self.meta = _init_meta() 
+        self.build = build
+        self.meta["gwaslab"]["set_name"] =  set
+        self.meta["gwaslab"]["species"] = species
+
+        # print gwaslab version information
+        _show_version(self.log,  verbose=verbose)
+
+        self.data = _extract_variant(variant_set, sumstats_dic,log=self.log, verbose=verbose)
+ 
+    def plot_effect(self,**args):
+        _plot_effect(self.data,**args)
+
+
+#### healper #################################################################################
+
+    def lookup_status(self,status="STATUS"):
+        return lookupstatus(self.data[status])
+    
+    def set_build(self, build, verbose=True):
+        self.data, self.meta["gwaslab"]["genome_build"] = _set_build(self.data, build=build, log=self.log,verbose=verbose)
+        gc.collect()
+
+    def infer_build(self,verbose=True,**kwargs):
+        self.data, self.meta["gwaslab"]["genome_build"] = inferbuild(self.data,log=self.log,verbose=verbose,**kwargs)
+    
+    def liftover(self,to_build, from_build=None,**kwargs):
+        if from_build is None:
+            if self.meta["gwaslab"]["genome_build"]=="99":
+                self.data, self.meta["gwaslab"]["genome_build"] = inferbuild(self.data,**kwargs)
+            from_build = self.meta["gwaslab"]["genome_build"]
+        self.data = parallelizeliftovervariant(self.data,from_build=from_build, to_build=to_build, log=self.log,**kwargs)
+        self.meta["is_sorted"] = False
+        self.meta["is_harmonised"] = False
+        self.meta["gwaslab"]["genome_build"]=to_build
+
+# QC ######################################################################################
+    #clean the sumstats with one line
+    def basic_check(self,
+                    remove=False,
+                    remove_dup=False,
+                    n_cores=1,
+                    fixid_args={},
+                    removedup_args={},
+                    fixchr_args={},
+                    fixpos_args={},
+                    fixallele_args={},
+                    sanitycheckstats_args={},
+                    consistencycheck_args={},
+                    normalize=True,
+                    normalizeallele_args={},
+                    verbose=True):
+        ###############################################
+        # try to fix data without dropping any information
+        self.data = fixID(self.data,log=self.log,verbose=verbose, **fixid_args)
+        self.data = fixchr(self.data,log=self.log,remove=remove,verbose=verbose,**fixchr_args)
+        self.data = fixpos(self.data,log=self.log,remove=remove,verbose=verbose,**fixpos_args)
+        self.data = fixallele(self.data,log=self.log,remove=remove,verbose=verbose,**fixallele_args)
+        self.data = sanitycheckstats(self.data,log=self.log,verbose=verbose,**sanitycheckstats_args)
+        _check_data_consistency(self.data,log=self.log,verbose=verbose,**consistencycheck_args)
+        
+        if normalize is True:
+            self.data = parallelnormalizeallele(self.data,n_cores=n_cores,verbose=verbose,log=self.log,**normalizeallele_args)
+        if remove_dup is True:
+            self.data = removedup(self.data,log=self.log,verbose=verbose,**removedup_args)
+        self.data = sortcoordinate(self.data,verbose=verbose,log=self.log)
+        self.data = sortcolumn(self.data,verbose=verbose,log=self.log)
+        self.meta["is_sorted"] = True
+        ###############################################
+        
+    
+    def harmonize(self,
+              basic_check=True,
+              ref_seq=None,
+              ref_rsid_tsv=None,
+              ref_rsid_vcf=None,
+              ref_infer=None,
+              ref_alt_freq=None,
+              maf_threshold=0.40,
+              ref_seq_mode="v",
+              n_cores=1,
+              remove=False,
+              checkref_args={},
+              removedup_args={},
+              assignrsid_args={},
+              inferstrand_args={},
+              flipallelestats_args={},
+              liftover_args={},
+              fixid_args={},
+              fixchr_args={},
+              fixpos_args={},
+              fixallele_args={},
+              sanitycheckstats_args={},
+              normalizeallele_args={}
+              ):
+        
+        #Standard pipeline
+        ####################################################
+        #part 1 : basic_check
+        #    1.1 fix ID
+        #    1.2 remove duplication
+        #    1.3 standardization : CHR POS EA NEA
+        #    1.4 normalization : EA NEA
+        #    1.5 sanity check : BETA SE OR EAF N OR_95L OR_95H
+        #    1.6 sorting genomic coordinates and column order 
+        if basic_check is True:
+            
+            self.data = fixID(self.data,log=self.log,**fixid_args)
+            
+            self.data = fixchr(self.data,remove=remove,log=self.log,**fixchr_args)
+            
+            self.data = fixpos(self.data,remove=remove,log=self.log,**fixpos_args)
+            
+            self.data = fixallele(self.data,log=self.log,**fixallele_args)
+            
+            self.data = sanitycheckstats(self.data,log=self.log,**sanitycheckstats_args)
+            
+            self.data = parallelnormalizeallele(self.data,log=self.log,n_cores=n_cores,**normalizeallele_args)
+            
+            self.data = sortcolumn(self.data,log=self.log)
+            
+            gc.collect()
+        
+        #####################################################
+        #part 2 : annotating and flipping
+        #    2.1  ref check -> flip allele and allel-specific stats
+        #    2.2  assign rsid
+        #    2.3 infer strand for palindromic SNP
+        #
+        ########## liftover ###############
+        #    3 : liftover by chr and pos to target build  -> reset status
+        ###################################
+        #   3.1 ref check (target build) -> flip allele and allel-specific stats  
+        #   3.2  assign rsid (target build)
+        #   3.2 infer strand for palindromic SNP (target build)
+        #####################################################
+        if ref_seq is not None:
+            if ref_seq_mode=="v":
+                self.data = checkref(self.data,ref_seq,log=self.log,**checkref_args)
+            elif ref_seq_mode=="s":
+                self.data = oldcheckref(self.data,ref_seq,log=self.log,**checkref_args)
+            else:
+                raise ValueError("ref_seq_mode should be 'v' (vectorized, faster) or 's' (sequential, slower)")
+            
+            self.meta["gwaslab"]["references"]["ref_seq"] = ref_seq
+            
+            self.data = flipallelestats(self.data,log=self.log,**flipallelestats_args)
+            
+            gc.collect()
+            
+        if ref_infer is not None: 
+            
+            self.data= parallelinferstrand(self.data,ref_infer = ref_infer,ref_alt_freq=ref_alt_freq,maf_threshold=maf_threshold,
+                                              n_cores=n_cores,log=self.log,**inferstrand_args)
+
+            self.meta["gwaslab"]["references"]["ref_infer"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_infer"] , ref_infer)
+            
+            self.data =flipallelestats(self.data,log=self.log,**flipallelestats_args)
+            
+            gc.collect()
+            
+        if (ref_seq is not None or ref_infer is not None) and (ref_rsid_tsv is not None or ref_rsid_vcf is not None):
+
+            self.data = fixID(self.data, log=self.log, **{"fixid":True, "fixsep":True, "overwrite":True})
+
+            gc.collect()
+        
+        #####################################################
+        if ref_rsid_tsv is not None:
+            
+            self.data = parallelizeassignrsid(self.data,path=ref_rsid_tsv,ref_mode="tsv",
+                                                 n_cores=n_cores,log=self.log,**assignrsid_args)
+            
+            
+
+            self.meta["gwaslab"]["references"]["ref_rsid_tsv"] = ref_rsid_tsv
+            gc.collect()
+
+        if ref_rsid_vcf is not None:
+            self.data = parallelizeassignrsid(self.data,path=ref_rsid_vcf,ref_mode="vcf",
+                                                 n_cores=n_cores,log=self.log,**assignrsid_args)   
+
+            self.meta["gwaslab"]["references"]["ref_rsid_vcf"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_rsid_vcf"] , ref_rsid_vcf)
+            
+            gc.collect()
+        ######################################################    
+        if remove is True:
+            
+            self.data = removedup(self.data,log=self.log,**removedup_args)
+        ################################################ 
+        
+        self.data = sortcoordinate(self.data,log=self.log)
+        
+        self.data = sortcolumn(self.data,log=self.log)
+        gc.collect()
+        self.meta["is_sorted"] = True
+        self.meta["is_harmonised"] = True
+        return self
+    ############################################################################################################
+    #customizable API to build your own QC pipeline
+    def fix_id(self,**kwargs):
+        self.data = fixID(self.data,log=self.log,**kwargs)
+    def flip_snpid(self,**kwargs):
+        self.data = flipSNPID(self.data,log=self.log,**kwargs)
+    def strip_snpid(self,**kwargs):
+        self.data = stripSNPID(self.data,log=self.log,**kwargs)
+    def fix_chr(self,**kwargs):
+        self.data = fixchr(self.data,log=self.log,**kwargs)
+    def fix_pos(self,**kwargs):
+        self.data = fixpos(self.data,log=self.log,**kwargs)
+    def fix_allele(self,**kwargs):
+        self.data = fixallele(self.data,log=self.log,**kwargs)
+    def remove_dup(self,**kwargs):
+        self.data = removedup(self.data,log=self.log,**kwargs)
+    def check_sanity(self,**kwargs):
+        self.data = sanitycheckstats(self.data,log=self.log,**kwargs)
+    def check_data_consistency(self, **kwargs):
+        _check_data_consistency(self.data,log=self.log,**kwargs)
+    def check_id(self,**kwargs):
+        pass
+    def check_ref(self,ref_seq,ref_seq_mode="v",**kwargs):
+        if ref_seq_mode=="v":
+            self.meta["gwaslab"]["references"]["ref_seq"] = ref_seq
+            self.data = checkref(self.data,ref_seq,log=self.log,**kwargs)
+        elif ref_seq_mode=="s":
+            self.meta["gwaslab"]["references"]["ref_seq"] = ref_seq
+            self.data = oldcheckref(self.data,ref_seq,log=self.log,**kwargs)            
+    def infer_strand(self,ref_infer,**kwargs):
+        self.meta["gwaslab"]["references"]["ref_infer"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_infer"] , ref_infer)
+        self.data = parallelinferstrand(self.data,ref_infer=ref_infer,log=self.log,**kwargs)
+    def flip_allele_stats(self,**kwargs):
+        self.data = flipallelestats(self.data,log=self.log,**kwargs)
+    def normalize_allele(self,**kwargs):
+        self.data = parallelnormalizeallele(self.data,log=self.log,**kwargs)
+    def assign_rsid(self,
+                    ref_rsid_tsv=None,
+                    ref_rsid_vcf=None,
+                    **kwargs):
+        if ref_rsid_tsv is not None:
+            self.data = parallelizeassignrsid(self.data,path=ref_rsid_tsv,ref_mode="tsv",log=self.log,**kwargs)
+            self.meta["gwaslab"]["references"]["ref_rsid_tsv"] = ref_rsid_tsv
+        if ref_rsid_vcf is not None:
+            self.data = parallelizeassignrsid(self.data,path=ref_rsid_vcf,ref_mode="vcf",log=self.log,**kwargs)   
+            self.meta["gwaslab"]["references"]["ref_rsid_vcf"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_rsid_vcf"] , ref_rsid_vcf)
+    def rsid_to_chrpos(self,**kwargs):
+        self.data = rsidtochrpos(self.data,log=self.log,**kwargs)
+    def rsid_to_chrpos2(self,**kwargs):
+        self.data = parallelrsidtochrpos(self.data,log=self.log,**kwargs)
+
+    ############################################################################################################
+    
+    def sort_coordinate(self,**sort_args):
+        self.data = sortcoordinate(self.data,log=self.log,**sort_args)
+        self.meta["is_sorted"] = True
+    def sort_column(self,**kwargs):
+        self.data = sortcolumn(self.data,log=self.log,**kwargs)
+    
+    ############################################################################################################
+    def fill_data(self, verbose=True, **kwargs):
+        self.data = filldata(self.data, verbose=verbose, log=self.log, **kwargs)
+        self.data = sortcolumn(self.data, verbose=verbose, log=self.log)
+
+# utilities ############################################################################################################
+    # filter series ######################################################################
+    def filter_flanking(self, inplace=False,**kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _get_flanking(new_Sumstats_object.data, **kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _get_flanking(self.data, **kwargs)
+    def filter_flanking_by_chrpos(self, chrpos,  inplace=False,**kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _get_flanking_by_chrpos(new_Sumstats_object.data, chrpos, **kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _get_flanking_by_chrpos(self.data, chrpos,**kwargs)
+    def filter_flanking_by_id(self, snpid, inplace=False,**kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _get_flanking_by_id(new_Sumstats_object.data, snpid, **kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _get_flanking_by_id(self.data, snpid, **kwargs)
+    def filter_value(self, expr, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = filtervalues(new_Sumstats_object.data,expr,log=new_Sumstats_object.log, **kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = filtervalues(self.data, expr,log=self.log,**kwargs)
+    def filter_out(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = filterout(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = filterout(self.data,log=self.log,**kwargs)
+    def filter_in(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = filterin(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = filterin(self.data,log=self.log,**kwargs)
+    def filter_region_in(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = filterregionin(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = filterregionin(self.data,log=self.log,**kwargs)
+    def filter_region_out(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = filterregionout(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = filterregionout(self.data,log=self.log,**kwargs)
+    def filter_palindromic(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _filter_palindromic(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _filter_palindromic(self.data,log=self.log,**kwargs)
+    def filter_snp(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _filter_snp(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _filter_snp(self.data,log=self.log,**kwargs)
+    def filter_indel(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _filter_indel(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _filter_indel(self.data,log=self.log,**kwargs)
+    
+    def exclude_hla(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _exclude_hla(new_Sumstats_object.data,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _exclude_hla(self.data,log=self.log,**kwargs)
+
+
+    def random_variants(self,inplace=False,n=1,p=None,**kwargs):
+        if inplace is True:
+            self.data = sampling(self.data,n=n,p=p,log=self.log,**kwargs)
+        else:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = sampling(new_Sumstats_object.data,n=n,p=p,log=new_Sumstats_object.log,**kwargs)
+            return new_Sumstats_object
+        
+    def filter_hapmap3(self, inplace=False, build=None, **kwargs ):
+        if build is None:
+            build = self.meta["gwaslab"]["genome_build"]
+        if inplace is True:
+            self.data = gethapmap3(self.data, build=build,log=self.log, **kwargs)
+        else:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = gethapmap3(new_Sumstats_object.data, build=build,log=self.log, **kwargs)
+            return new_Sumstats_object
+    ######################################################################
+    
+    def check_af(self,ref_infer,**kwargs):
+        self.data = parallelecheckaf(self.data,ref_infer=ref_infer,log=self.log,**kwargs)
+        self.meta["gwaslab"]["references"]["ref_infer_daf"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_infer_daf"] , ref_infer)
+    
+    def infer_af(self,ref_infer,**kwargs):
+        self.data = paralleleinferaf(self.data,ref_infer=ref_infer,log=self.log,**kwargs)
+        self.meta["gwaslab"]["references"]["ref_infer_af"] = ref_infer
+        self.meta["gwaslab"]["references"]["ref_infer_af"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_infer_af"] , ref_infer)
+    def maf_to_eaf(self,ref_infer,**kwargs):
+        self.data = _paralleleinferafwithmaf(self.data,ref_infer=ref_infer,log=self.log,**kwargs)
+        self.meta["gwaslab"]["references"]["ref_infer_maf"] = ref_infer
+        self.meta["gwaslab"]["references"]["ref_infer_maf"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_infer_af"] , ref_infer)    
+    def plot_daf(self, **kwargs):
+        fig,outliers = plotdaf(self.data, **kwargs)
+        return fig, outliers
+    
+    def plot_gwheatmap(self, **kwargs):
+        fig = _gwheatmap(self.data, **kwargs)
+        return fig
+    
+    def plot_mqq(self, build=None, **kwargs):
+
+        chrom="CHR"
+        pos="POS"
+        p="P"
+        
+        if "SNPID" in self.data.columns:
+            snpid="SNPID"
+        elif "rsID" in self.data.columns:
+            snpid="rsID"
+        
+        if "EAF" in self.data.columns:
+            eaf="EAF"
+        else:
+            eaf=None
+
+        # extract build information from meta data
+        if build is None:
+            build = self.meta["gwaslab"]["genome_build"]
+
+        plot = mqqplot(self.data,
+                       snpid=snpid, 
+                       chrom=chrom, 
+                       pos=pos, 
+                       p=p, 
+                       eaf=eaf,
+                       build = build, 
+                       **kwargs)
+        
+        return plot
+    
+    def plot_trumpet(self, build=None, **kwargs):
+        if build is None:
+            build = self.meta["gwaslab"]["genome_build"]
+        fig = plottrumpet(self.data,build = build,  **kwargs)
+        return fig
+
+    def get_lead(self, build=None, gls=False, **kwargs):
+        if "SNPID" in self.data.columns:
+            id_to_use = "SNPID"
+        else:
+            id_to_use = "rsID"
+        
+        # extract build information from meta data
+        if build is None:
+            build = self.meta["gwaslab"]["genome_build"]
+        
+        output = getsig(self.data,
+                           id=id_to_use,
+                           chrom="CHR",
+                           pos="POS",
+                           p="P",
+                           log=self.log,
+                           build=build,
+                           **kwargs)
+        # return sumstats object    
+        if gls == True:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = output
+            gc.collect()
+            return new_Sumstats_object
+        return output
+
+    def get_density(self, sig_list=None, windowsizekb=100,**kwargs):
+        
+        if "SNPID" in self.data.columns:
+            id_to_use = "SNPID"
+        else:
+            id_to_use = "rsID"
+        
+        if sig_list is None:
+            self.data["DENSITY"] = getsignaldensity(self.data,
+                                                    id=id_to_use,
+                                                    chrom="CHR",
+                                                    pos="POS",
+                                                    bwindowsizekb=windowsizekb,
+                                                    log=self.log)
+        else:
+            if isinstance(sig_list, pd.DataFrame):
+                self.data["DENSITY"] = assigndensity(self.data,
+                                                    sig_list,
+                                                    id=id_to_use, 
+                                                    chrom="CHR", 
+                                                    pos="POS", 
+                                                    bwindowsizekb=windowsizekb,
+                                                    log=self.log)
+
+        
+    def get_novel(self, **kwargs):
+        if "SNPID" in self.data.columns:
+            id_to_use = "SNPID"
+        else:
+            id_to_use = "rsID"
+        output = getnovel(self.data,
+                           id=id_to_use,
+                           chrom="CHR",
+                           pos="POS",
+                           p="P",
+                           log=self.log,
+                           **kwargs)
+        # return sumstats object    
+        return output
+    
+    def check_cis(self, gls=False, **kwargs):
+        if "SNPID" in self.data.columns:
+            id_to_use = "SNPID"
+        else:
+            id_to_use = "rsID"
+        output = _check_cis(self.data,
+                           id=id_to_use,
+                           chrom="CHR",
+                           pos="POS",
+                           p="P",
+                           log=self.log,
+                           **kwargs)
+        
+        # return sumstats object   
+        if gls == True:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = output
+            gc.collect()
+            return new_Sumstats_object
+        return output
+    
+    def check_novel_set(self, **kwargs):
+        if "SNPID" in self.data.columns:
+            id_to_use = "SNPID"
+        else:
+            id_to_use = "rsID"
+        output = _check_novel_set(self.data,
+                           id=id_to_use,
+                           chrom="CHR",
+                           pos="POS",
+                           p="P",
+                           log=self.log,
+                           **kwargs)
+        # return sumstats object    
+        return output
+    
+    def anno_gene(self, **kwargs):
+        if "SNPID" in self.data.columns:
+            id_to_use = "SNPID"
+        else:
+            id_to_use = "rsID"
+        output = annogene(self.data,
+                           id=id_to_use,
+                           chrom="CHR",
+                           pos="POS",
+                           log=self.log,
+                           **kwargs)
+        return output
+        
+    def get_per_snp_r2(self,**kwargs):
+        self.data = _get_per_snp_r2(self.data, beta="BETA", af="EAF", n="N", log=self.log, **kwargs)
+        #add data inplace
+
+
+# to_format ###############################################################################################       
+
+    def to_format(self, path, build=None, verbose=True, **kwargs):
+        if build is None:
+            build = self.meta["gwaslab"]["genome_build"]
+        _to_format(self.data, path, log=self.log, verbose=verbose, meta=self.meta, build=build, **kwargs)
+
+ 

gwaslab/g_version.py

@@ -15,8 +15,8 @@ def _get_version():
 def gwaslab_info():
     # version meta information
     dic={
-   "version":"3.5.5",
-   "release_date":"20250102"
+   "version":"3.5.6",
+   "release_date":"20250306"
     }
     return dic