Broken error handling in multithread_codonalign_build

[revinici]

For some reason there was an IndexError when running the method below, but since the variable codon_alignment was never initialized there was a UnboundLocalError raised as well claiming: local variable 'codon_alignment' referenced before assignment

I am not sure why there was an index error, but can this method be updated so that it gracefully continues? I will have to run the code with the problem inputs in the debugger to investigate the index error.

I am using panaroo version 1.5.

panaroo/panaroo/generate_alignments.py

Lines 324 to 337 in e928a7a

	def multithread_codonalign_build(dna, protein, name):
	try:
	codon_alignment = codonalign.build(dna, protein)
	except RuntimeError as e:
	print(e)
	print(name)
	print(dna)
	print(protein)
	except IndexError as e:
	print(e)
	print(name)
	print(dna)
	print(protein)
	return(name, codon_alignment)

[revinici]

Hello, I investigated the cause of the index error by passing the problem aligned protein FASTA and unaligned dna FASTA to Bio.codonalign.build and I got the stack trace below. It appears that there are some mistranslation issues in addition to a mismatch between refound dna and protein sequences. I think that until this get solved I will turn off codon alignments.

/home/user/miniconda3/envs/panaroo/lib/python3.9/site-packages/Bio/codonalign/__init__.py:627: BiopythonWarning: GENOME_ID_1;1243_20_0(M 0) does not correspond to GENOME_ID_1;1243_20_0(GTG)
  warnings.warn(
/home/user/miniconda3/envs/panaroo/lib/python3.9/site-packages/Bio/codonalign/__init__.py:627: BiopythonWarning: GENOME_ID_2;1490_12_0(M 0) does not correspond to GENOME_ID_2;1490_12_0(GTG)
  warnings.warn(
/home/user/miniconda3/envs/panaroo/lib/python3.9/site-packages/Bio/codonalign/__init__.py:627: BiopythonWarning: GENOME_ID_3;1609_19_51(M 0) does not correspond to GENOME_ID_3;1609_19_51(TTG)
  warnings.warn(
/home/user/miniconda3/envs/panaroo/lib/python3.9/site-packages/Bio/codonalign/__init__.py:382: BiopythonWarning: middle frameshift detection failed for GENOME_ID_4;101_refound_2380
  warnings.warn(
Traceback (most recent call last):
  File "/local/home/user/.pycharm_helpers/pydev/pydevd.py", line 1551, in _exec
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "/local/home/user/.pycharm_helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/tmp/pycharm_project_499/panaroo/bug.py", line 30, in <module>
    codon_alignment = codonalign.build(protein, dna)# load the final pangenome graph
  File "/home/user/miniconda3/envs/panaroo/lib/python3.9/site-packages/Bio/codonalign/__init__.py", line 169, in build
    corr_span = _check_corr(
  File "/home/user/miniconda3/envs/panaroo/lib/python3.9/site-packages/Bio/codonalign/__init__.py", line 435, in _check_corr
    raise RuntimeError(
RuntimeError: Protein SeqRecord (GENOME_ID_4;101_refound_2380) and Nucleotide SeqRecord (GENOME_ID_4;101_refound_2380) do not match!

[nzmacalasdair]

Hello,

Apologies for the delay in getting to this, it doesn't look like any error we've seen before in the codon alignment module. Would it be possible for you to share some toy data from which we can reproduce this error?

Many thanks,

Neil