ImportError: Bio.Alphabet has been removed from Biopython

Question

[Neel]

Hi, i am trying to run IS Associated with Antibiotic Resistance Genes Finder tool and it give following error.

./ISAbR-0.1.6.py
./ISAbR-0.1.6.py:219: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if character is 'T':
./ISAbR-0.1.6.py:221: SyntaxWarning: "is" with a literal. Did you mean "=="?
  elif character is 'A':
./ISAbR-0.1.6.py:223: SyntaxWarning: "is" with a literal. Did you mean "=="?
  elif character is 'C':
./ISAbR-0.1.6.py:225: SyntaxWarning: "is" with a literal. Did you mean "=="?
  elif character is 'G':
./ISAbR-0.1.6.py:227: SyntaxWarning: "is" with a literal. Did you mean "=="?
  elif character is 'N':
./ISAbR-0.1.6.py:238: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if strands[0] is '-':
./ISAbR-0.1.6.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if strands[1] is '-':
./ISAbR-0.1.6.py:262: SyntaxWarning: "is" with a literal. Did you mean "=="?
  if item[3] is '+':
./ISAbR-0.1.6.py:265: SyntaxWarning: "is" with a literal. Did you mean "=="?
  elif item[3] is '-':
Traceback (most recent call last):
  File "./ISAbR-0.1.6.py", line 33, in <module>
    from Bio.Alphabet import IUPAC
  File "/home/bvs/.local/lib/python3.8/site-packages/Bio/Alphabet/__init__.py", line 20, in <module>
    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!

[Wayne]

There is advice built in to the error report of several options to try to fix this. Did you try any of that?
If you wanted more guidance, you'd have to be more forthcoming about the source of ISAbR-0.1.6.py. For example a link to the repository of the software? The associated publication describing it? Searches with the limited information you provide comes up with nothing that specifically points at a good lead to this software.

One reason that providing more information may help is that the developers may have already fixed this or provided a workaround for those not wishing to troubleshoot themselves. With what you've provided, it doesn't seem feasible to check into this.

Plus, your title should specify the program giving your the error, not just the generic error message triggered.