ImportError: Bio.Alphabet has been removed from Biopython.

[neelam19051]

.Hi, I am facing this error and i followed below instruction also but still unable to solve it. /TnComp_finder.py ./TnComp_finder.py:247: SyntaxWarning: "is" with a literal. Did you mean "=="? if character is 'T': ./TnComp_finder.py:249: SyntaxWarning: "is" with a literal. Did you mean "=="? elif character is 'A': ./TnComp_finder.py:251: SyntaxWarning: "is" with a literal. Did you mean "=="? elif character is 'C': ./TnComp_finder.py:253: SyntaxWarning: "is" with a literal. Did you mean "=="? elif character is 'G': ./TnComp_finder.py:255: SyntaxWarning: "is" with a literal. Did you mean "=="? elif character is 'N': ./TnComp_finder.py:275: SyntaxWarning: "is" with a literal. Did you mean "=="? if item[3] is '+': ./TnComp_finder.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? elif item[3] is '-': Traceback (most recent call last): File "./TnComp_finder.py", line 31, in from Bio.Alphabet import IUPAC File "/home/bvs/.local/lib/python3.8/site-packages/Bio/Alphabet/init.py", line 20, in raise ImportError( ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

Thank you!

[Holert]

From https://biopython.org/wiki/Alphabet

Try removing the references to Alphabet from the script:

Line 31: remove "from Bio.Alphabet import IUPAC" Line 438: change "gbk_record = SeqRecord(Seq(sequence, IUPAC.unambiguous_dna)" to "gbk_record = SeqRecord(Seq(sequence)"

[pengxyii]

Hello, I use tncomp_finder on a archaeal genome，and facing this error: Traceback (most recent call last): File "/home/pengxy/mambaforge/envs/tncomp_finder/lib/python3.12/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) ^^^^^^^^^^^^^^^^^^^ File "/home/pengxy/mambaforge/envs/tncomp_finder/lib/python3.12/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) ^^^^^^^^^^^^^^^^ File "/home/pengxy/data/software/tncomp_finder/TnComp_finder.py", line 170, in parse_blastn write_report(candidates, outdir) File "/home/pengxy/data/software/tncomp_finder/TnComp_finder.py", line 326, in write_report seq_info.update({key:[transposon, extended_seq]}) ^^^^^^^^^^^^ UnboundLocalError: cannot access local variable 'extended_seq' where it is not associated with a value """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/pengxy/data/software/tncomp_finder/TnComp_finder.py", line 609, in main() File "/home/pengxy/data/software/tncomp_finder/TnComp_finder.py", line 598, in main Pool(args.processors).map(partial(parse_blastn, outdir=args.out), args.files) File "/home/pengxy/mambaforge/envs/tncomp_finder/lib/python3.12/multiprocessing/pool.py", line 367, in map return self._map_async(func, iterable, mapstar, chunksize).get() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pengxy/mambaforge/envs/tncomp_finder/lib/python3.12/multiprocessing/pool.py", line 774, in get raise self._value UnboundLocalError: cannot access local variable 'extended_seq' where it is not associated with a value

Do you know why that is? Thank you