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)')