e0df390fc7750251ab187beaf5523ae529e6a30f gperez2 Sat Mar 29 16:13:43 2025 -0700 Fixing SyntaxWarning: invalid escape sequence '\G' by doubling '\G', No RM diff --git src/utils/qa/pairLastzWrapper.py src/utils/qa/pairLastzWrapper.py index a8a16cdb715..e6c8e55d2ae 100755 --- src/utils/qa/pairLastzWrapper.py +++ src/utils/qa/pairLastzWrapper.py @@ -89,33 +89,33 @@ else: clade='other' else: chromSizes_1="/hive/data/genomes/"+assembly+"/chrom.sizes" try: bash('ls '+chromSizes_1) #print(bash('ls '+chromSizes_1)) except subprocess.CalledProcessError: sys.stdout = sys.__stdout__ print('ls: cannot access '+chromSizes_1+': No such file or directory') quit() digit_pos= re.search(r"\d", assembly) db_edit = assembly[0:digit_pos.start()] if db_edit in primates: clade='primate' else: - db = bash("hgsql -e \"select genome from dbDb where name='"+assembly+"'\G\" hgcentraltest | grep genome | cut -c 9-") + db = bash("hgsql -e \"select genome from dbDb where name='"+assembly+"'\\G\" hgcentraltest | grep genome | cut -c 9-") db = str(db)[1:-1] - db = bash("hgsql -e \"select clade from genomeClade where genome="+db+"\G\" hgcentraltest | grep clade | cut -c 8-") + db = bash("hgsql -e \"select clade from genomeClade where genome="+db+"\\G\" hgcentraltest | grep clade | cut -c 8-") db = str(db)[2:-2] if db in validClades: clade=db else: clade='other' return clade def getAssembly(assembly): """Input assembly and return native assembly or GC assembly name""" if assembly[0:3]=='GCA' or assembly[0:3]=='GCF': gcAssembly=goto(assembly) return gcAssembly else: return assembly def scoringScheme(assembly):