Mercurial > repos > p.lucas > taxid_genusexpand_taxid2acc

comparison TAXID_genusexpand_taxid2acc.py @ 9:7e75c71e3c8e draft

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Uploaded 13 03 23 fin def load_taxids fix bug to avoid error with empty line
author p.lucas
date Mon, 13 Mar 2023 16:16:49 +0000
parents 8c9418230a5a
children 5a4ac43fea68
comparison
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8:8c9418230a5a 9:7e75c71e3c8e
190 " file does not exist, line "+ str(sys._getframe().f_lineno) ) 190 " file does not exist, line "+ str(sys._getframe().f_lineno) )
191 191
192 cmd = "cut -f 1,2 "+taxid_acc_tabular_f+" | sort | uniq " 192 cmd = "cut -f 1,2 "+taxid_acc_tabular_f+" | sort | uniq "
193 193
194 for line in os.popen(cmd).readlines(): 194 for line in os.popen(cmd).readlines():
195 if line != "":
196 continue
195 k, v = line.rstrip().split() 197 k, v = line.rstrip().split()
196 taxidlist.append(k) 198 taxidlist.append(k)
197 accnrlist.append(v) 199 accnrlist.append(v)
198 200
199 return taxidlist 201 return taxidlist