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Fixed the SCSA error when pandas>2 (#174) (#232) (#168) (#214)
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@Starlitnightly
Starlitnightly committed Dec 18, 2024
1 parent 44144f5 commit 0d8cab9
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Showing 3 changed files with 476 additions and 165 deletions.
88 changes: 72 additions & 16 deletions omicverse/single/_SCSA.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,8 +111,13 @@ def to_output(h_values,wb,outtag,cname,title):
if outtag.lower() == "ms-excel":
h_values.to_excel(wb,sheet_name = "Cluster " + cname + " " + title,index=False)
else:
h_values.to_csv(wb,sep="\t",quotechar = "\t",index=False,header=False)
pass
def clean_non_printable_chars(value):
"""移除字符串中的非打印字符"""
if isinstance(value, str):
return ''.join(c for c in value if c.isprintable())
return value
h_values = h_values.applymap(clean_non_printable_chars)
h_values.to_csv(wb,sep="\t",quotechar = "\t",index=False,header=False,encoding='gbk')

@staticmethod
def translate_go(name="go.obo"):
Expand All @@ -138,10 +143,23 @@ def translate_go(name="go.obo"):

def do_go_annotation(self,gof,fore,back,cname,gtype):
"""return go annotation with significance tag"""
fil = gof[2].map(lambda value: len(set([value]) & fore) > 0)
fgnames = gof[fil].groupby(by=4)[2].unique()
bfil = gof[2].map(lambda value: len(set([value]) & back) > 0)
bgnames = gof[bfil].groupby(by=4)[2].unique()

if self.year == 2024:
fil = gof['2'].map(lambda value: len(set([value]) & fore) > 0)
fgnames = gof[fil].groupby(by="4")["2"].unique()
bfil = gof["2"].map(lambda value: len(set([value]) & back) > 0)
bgnames = gof[bfil].groupby(by="4")["2"].unique()
elif self.year == 2023:
fil = gof[2].map(lambda value: len(set([value]) & fore) > 0)
fgnames = gof[fil].groupby(by=4)[2].unique()
bfil = gof[2].map(lambda value: len(set([value]) & back) > 0)
bgnames = gof[bfil].groupby(by=4)[2].unique()
else:
fil = gof[2].map(lambda value: len(set([value]) & fore) > 0)
fgnames = gof[fil].groupby(by=4)[2].unique()
bfil = gof[2].map(lambda value: len(set([value]) & back) > 0)
bgnames = gof[bfil].groupby(by=4)[2].unique()

dat = DataFrame({"genes":fgnames,"othergenes":bgnames})
num1 = len(fore)
num2 = len(back)
Expand Down Expand Up @@ -338,9 +356,9 @@ def calcu_cellranger_group(self,expfile,hgvc=False):
self.wb = ExcelWriter(self.output)
self.wbgo = self.wb
elif self.outfmt.lower() == "txt":
self.wb = open(self.output,"w")
self.wb = open(self.output,"w", encoding='utf-8')
self.wb.write("Cell Type\tZ-score\tCluster\n")
self.wbgo = open(self.output + ".go","w")
self.wbgo = open(self.output + ".go","w", encoding='utf-8')
self.wbgo.write('ids\tgene_num\tothergene_num\tp-value\tq-value\tsig\tname\tcluster\tgo_class\n')
else:
print("Error output format: -m, --outfmt,(ms-excel,[txt])")
Expand Down Expand Up @@ -461,12 +479,12 @@ def calcu_seurat_group(self,expfile,hgvc=False):
self.wb = ExcelWriter(self.output)
self.wbgo = self.wb
elif self.outfmt.lower() == "txt":
self.wb = open(self.output,"w")
self.wb = open(self.output,"w", encoding='utf-8')
if self.target == "cancersea":
self.wb.write("Cell Type\tZ-score\tCluster\n")
else:
self.wb.write("Cell Type\tZ-score\tCluster\n")
self.wbgo = open(self.output + ".go","w")
self.wbgo = open(self.output + ".go","w", encoding='utf-8')
self.wbgo.write('ids\tgene_num\tothergene_num\tp-value\tq-value\tsig\tname\tcluster\tgo_class\n')
else:
print("Error output format: -m, -outfmt,(ms-excel,[txt])")
Expand Down Expand Up @@ -587,12 +605,12 @@ def calcu_scanpy_group(self,expfile,hgvc=False):
self.wb = ExcelWriter(self.output)
self.wbgo = self.wb
elif self.outfmt.lower() == "txt":
self.wb = open(self.output,"w")
self.wb = open(self.output,"w", encoding='utf-8')
if self.target == "cancersea":
self.wb.write("Cell Type\tZ-score\tCluster\n")
else:
self.wb.write("Cell Type\tZ-score\tCluster\n")
self.wbgo = open(self.output + ".go","w")
self.wbgo = open(self.output + ".go","w", encoding='utf-8')
self.wbgo.write('ids\tgene_num\tothergene_num\tp-value\tq-value\tsig\tname\tcluster\tgo_class\n')
else:
print("Error output format: -m, -outfmt,(ms-excel,[txt])")
Expand Down Expand Up @@ -730,12 +748,12 @@ def calcu_scran_group(self,expfile,hgvc=False):
self.wb = ExcelWriter(self.output)
self.wbgo = self.wb
elif self.outfmt.lower() == "txt":
self.wb = open(self.output,"w")
self.wb = open(self.output,"w", encoding='utf-8')
if self.target == "cancersea":
self.wb.write("Cell Type\tZ-score\tCluster\n")
else:
self.wb.write("Cell Type\tZ-score\tCluster\n")
self.wbgo = open(self.output + ".go","w")
self.wbgo = open(self.output + ".go","w", encoding='utf-8')
self.wbgo.write('ids\tgene_num\tothergene_num\tp-value\tq-value\tsig\tname\tcluster\tgo_class\n')
else:
print("Error output format: -m, -outfmt,(ms-excel,[txt])")
Expand Down Expand Up @@ -1153,9 +1171,42 @@ def read_user_markers(self,colname):
if self.noprint == False:
print("User cells:", len(self.usermarkers['cellName'].unique()))
print("User genes:", len(self.usermarkers[colname].unique()))

def save_pickle_module(self, db):
"""save whole database"""
handler = gzip.open(db, "wb")
dump(self.gos, handler)
dump(self.human_gofs, handler)
dump(self.mouse_gofs, handler)
dump(self.cmarkers, handler)
dump(self.smarkers, handler)
dump(self.snames, handler)
dump(self.ensem_hgncs, handler)
dump(self.ensem_mouse, handler)

if 'plus' in db:
dump(self.pmarkers, handler)
else:
dump(self.smarkers, handler)

handler.close()

def load_pickle_module(self,db):
"""read whole database"""
if '2023' in db:
self.year=2023
if pd.__version__ > "1.5.3":
print("2023 database build on pandas<2, please downgrade your pandas version!")
raise ValueError("2023 database build on pandas<2, please downgrade your pandas version!")
elif '2024' in db:
self.year=2024
if pd.__version__ <= "1.5.3":
print("2024 database build on pandas>2 or higher, please update your pandas version!")
raise ValueError("2024 database build on pandas>2 or higher, please update your pandas version!")
else:
self.year=2023
print("Your database version is unknown, please check your database version!")

handler = gzip.open(db,"rb")
self.gos = load(handler)
self.human_gofs = load(handler)
Expand All @@ -1178,9 +1229,14 @@ def load_pickle_module(self,db):
if self.cellrange!=None:
self.cmarkers = self.cmarkers[self.cmarkers['cellName'].str.contains(self.cellrange)]
#self.smarkers = self.smarkers[~self.smarkers['cellName'].isin(fil)]

#if self.noprint == False:
print("Version V2.1 [2023/06/27]")
if self.year == 2023:
print("Version V2.1 [2023/06/27]")
elif self.year == 2024:
print("Version V2.2 [2024/12/18]")
else:
print("Unknown version")
if 'plus' not in db:
print("DB load: GO_items:{},Human_GO:{},Mouse_GO:{},\nCellMarkers:{},CancerSEA:{},\nEnsembl_HGNC:{},Ensembl_Mouse:{}".format(
len(self.gos),len(self.human_gofs),len(self.mouse_gofs),len(self.cmarkers),len(self.smarkers),len(self.ensem_hgncs),len(self.ensem_mouse))
Expand Down
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