Biopython DeprecationWarning for ungap() Method

[monserrj]

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:

1. Obtain the FASTA sequence for the PduK protein reference B1VB70 from UniProt.
2. Use Biopython to read the sequence and perform a sequence operation that involves the deprecated ungap() method, e.g., myseq.ungap("-").
3. 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

ncfp Version: https://github.com/widdowquinn/ncfp.git

Python Version: 3.9.0

Operating System: Windows10

[widdowquinn]

Thanks @monserrj

This is now fixed with b139660