def saveUCLA_id_ls(self,UCLA_id_ls,exist_action):
fname = os.path.join(self.projectDir,'UCLA_ids.tsv')
if exist_action=='check':
if os.path.isfile(fname):
return True
else:
return False
elif exist_action=='p':
if os.path.isfile(fname):
pass
else:
with open(fname, 'w') as f:
writ=csv.writer(f, delimiter='\t')
writ.writerow(UCLA_id_ls)
del writ
elif exist_action=='w':
with open(fname, 'w') as f:
writ=csv.writer(f, delimiter='\t')
writ.writerow(UCLA_id_ls)
del writ
else:
raise hs.hsError('variable existAction must be w (overwrite) or p (pass) or check')
def saveVCFfilename_ls(self,VCFfilename_ls,contig_ls,genotypeMethodID,exist_action):
fname = os.path.join(self.projectDir,'VCF_filename_ls_Meth'+str(genotypeMethodID)+'.tsv')
if exist_action=='check':
if os.path.isfile(fname):
return True
else:
return False
elif exist_action=='p':
if os.path.isfile(fname):
pass
else:
with open(fname, 'w') as f:
writer=csv.writer(f, delimiter='\t')
writer.writerow(VCFfilename_ls)
writer.writerow(contig_ls)
del writer
elif exist_action=='w':
with open(fname, 'w') as f:
writer=csv.writer(f, delimiter='\t')
writer.writerow(VCFfilename_ls)
writer.writerow(contig_ls)
del writer
else:
raise hs.hsError('variable existAction must be w (overwrite) or p (pass) or check')
def saveVCFInd(self,VCF_index_ls,genotype_method_id,exist_action):
"""
exist_action...
'w'... overwrite existing file
'p'... pass if the file exists
description_str... string describing the aim of this analysis, with trailing \n
"""
fname = os.path.join(self.projectDir,'VCF_indices_Meth'+str(genotype_method_id)+'.tsv')
if exist_action=='p':
if os.path.isfile(fname):
pass
else:
with open(fname, 'w') as f:
writ=csv.writer(f, delimiter='\t')
writ.writerow(VCF_index_ls)
del writ
elif exist_action=='w':
with open(fname, 'w') as f:
writ=csv.writer(f, delimiter='\t')
writ.writerow(VCF_index_ls)
del writ
else:
raise hs.hsError('variable existAction must be w (overwrite) or p (pass)')