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widdowquinn / ncfp

Program and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.

Home Page:https://widdowquinn.github.io/ncfp/

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Biopython DeprecationWarning for ungap() Method

monserrj opened this issue · comments

commented

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

commented

Thanks @monserrj

This is now fixed with b139660