Biopython DeprecationWarning for ungap() Method
monserrj opened this issue · comments
Summary:
BiopythonDeprecationWarning for theungap()
method, advising replacement with replace()
.
Description:
The code is currently using the deprecated ungap()
method in Biopython, which triggers a BiopythonDeprecationWarning. The warning suggests replacing myseq.ungap(gap)
with myseq.replace(gap, "")
to address the deprecation.
Reproducible Steps:
- Obtain the FASTA sequence for the PduK protein reference B1VB70 from UniProt.
- Use Biopython to read the sequence and perform a sequence operation that involves the deprecated
ungap()
method, e.g.,myseq.ungap("-")
. - Observe the BiopythonDeprecationWarning generated.
Current Output:
The correct output is generated with the warning.
Expected Output:
No warning should be generated, and the code should execute without issues