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Fix the errors in the Tutorial's codon-alignment section - #270
Doc/Tutorial/chapter_pairwise.rst, codon-alignment section. Six errors that came in with #266 from biopython/biopython#5376:
The E. coli "extract rows" block now uses alignment_ecoli and shows its real rows: 'SDVLRGYL-DYDAKKER', the full 49-nt sequence, and 49. The sentence above it describes the +1 frameshift (a skipped nucleotide, with a gap in the amino-acid row) instead of the HIV -1 story. The extra blank line that kept Tests/test_Tutorial.py from extracting the block is gone, so the block is now tested.
len(alignments) after protein_alignments = protein_aligner.align(...) is now len(protein_alignments). It passed by accident: the HIV iterator was still in scope and also has length 1.
The CodonAligner parameter paragraph points at table:codonalign-mnemonics, the table that follows it, not the pairwise-aligner table.
"proteina" and "rguments" fixed.
The dN/dS example no longer attributes LWL85's numbers to YN00. The ML block keeps its values to three decimals (0.083... 0.281...), and a sentence says why: the estimates come from a numerical optimization, and YN00 is left out because on this alignment calculate_dn_ds currently returns None. The block stays outside the doctest, as upstream had it: ML and YN00 import scipy, which the 3.14, ARM and PyPy CI jobs do not install (the second push made it a cont-doctest and those jobs failed; the third push reverted that).
Also from #5376, cosmetic: "the number of alignment amino acids" twice, now "aligned", and the dead nuc_ecoli = Seq(...) line that the next statement overwrote.
Five older slips in the same section, from the 2024 text: calculate_dN_dS "method" is the calculate_dn_ds function; "and input" is "as input"; calculate_dn_ds_matrix takes method and codon_table, not "only codon_table"; the trees are built "from these two matrices", not sequences; "Mcdonald" is "McDonald".
UPSTREAM.md gains row 41 (the documentation defects, queued) and row 42 (_yn00 returning None, with the two root causes, not fixed here, related to biopython/biopython#1611).
Why not fix the code too
_yn00 has two real defects on this input (a normalisation loop that stops at the shorter dict and leaves the initial kappa at -35, and a zero path-probability sum for a three-difference codon pair) and then falls off the end of its loop and returns None. What it should do instead is a behaviour choice, and the two YN00 lines already in the October list say its counting needs checking against PAML's yn00.c first. Row 42 records all three. Separate PR.
Testing
python -m pytest test_Tutorial.py --offline in a clean venv of this branch's code (/tmp/venv-sync, Python 3.12, scipy 1.18.1): 1 passed. Checked by name that the E. coli block and the len(protein_alignments) line are in the extracted doctest now; the ML block is not, on purpose.
Precision of the ML block: a clean run gives dN 0.0830393 and dS 0.2816991; the numbers upstream printed were 0.083040 and 0.281696, so L-BFGS-B drifts at the sixth decimal between machines. Three decimals is what a reader can rely on.
Real outputs for the E. coli rows and all four dN/dS methods captured by running the tutorial's own setup; _yn00 traced over its 20 passes (NaN throughout), and rerun with the normalisation loop corrected to confirm it still returns None.
pre-commit run --files Doc/Tutorial/chapter_pairwise.rst UPSTREAM.md: rstcheck, doc8, codespell, blacken-docs pass.
Upstream master (f10e88c58, 2026-10-28) has no commits to this chapter or to Bio/Align/analysis.py since #5376; its tracker has nothing on these.
Corrections to the first version of this PR
A verification pass found three mistakes in my first push: the RuntimeWarning I listed under "Noticed" as coming from ML is YN00's (ML is silent; now in row 42); the ML block's dS was off at the sixth decimal as well as its dN; and there was a sixth copy-paste error, the len(alignments) line.
Noticed, not done
Nothing. #5376's chapter diff has two hunks outside this section (a caption at line 812 and the dN/dS tree block); the tree block is inside the passing doctest, the caption was read only.
Updated the pairwise-alignment tutorial with corrected alignment examples, including the skipped nucleotide’s gap in the amino-acid row.
Corrected a protein-alignment example and clarified the reported dN/dS estimates, the None result for the documented YN00 case, and optional arguments for calculating dN/dS matrices.
The section rewritten upstream in biopython/biopython#5376 and merged here
in #266 showed the HIV Gag-Pol rows under the E. coli PrfB heading (the
block was a copy that still read `alignment`, and an extra blank line kept
test_Tutorial.py from ever extracting it), pointed at the pairwise-aligner
mnemonics table instead of the codon one, had two typos, and labelled
LWL85's dN/dS numbers as YN00 output. On that alignment YN00 returns None,
so the example now shows ML only and says why YN00 is left out.
Record both the documentation defects and the silent None from _yn00 in
UPSTREAM.md (rows 41 and 42). Fixes#269.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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Doc/Tutorial/chapter_pairwise.rst
Walkthrough
The tutorial’s codon-alignment references, examples, and dN/dS documentation were corrected. UPSTREAM.md records two queued reports, including the unresolved YN00 None result.
Changes: Codon-alignment tutorial
Layer / File(s)
Summary
Codon-alignment examples and references Doc/Tutorial/chapter_pairwise.rst
The tutorial corrects the mnemonic reference, wording, E. coli +1 frameshift example, and protein-alignment length check.
dN/dS documentation and reports Doc/Tutorial/chapter_pairwise.rst, UPSTREAM.md
The tutorial updates dN/dS output and argument descriptions. It states that YN00 returns None for this alignment. UPSTREAM.md adds reports about the tutorial defects and YN00 behavior.
dbolser/BioPAIthon#269: This PR corrects the codon-alignment tutorial defects described in the issue. It does not fix the separate _yn00 behavior.
Possibly related PRs
dbolser/BioPAIthon#266: PR #266 introduced the tutorial content that this PR corrects. This PR also documents the YN00 None result.
Suggested reviewers:mdehoon
Merge Risk: Low · previous review a8bf7
The PR is mergeable with a small documentation clarification; no runtime behavior is affected.
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The title clearly and concisely describes the main change: correcting errors in the Tutorial's codon-alignment section.
Linked Issues check
PR #269 requirements are met. Doc/Tutorial/chapter_pairwise.rst now uses alignment_ecoli, shows the correct rows, describes the +1 frameshift, and exposes the block to Tests/test_Tutorial.py. It…
Out of Scope Changes check
The changes stay within issue #269. The tutorial edits correct the requested codon-alignment examples and wording. The UPSTREAM.md rows record the related documentation and separate _yn00 defects.…
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No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentat…
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Explanation
PR #269 requirements are met. Doc/Tutorial/chapter_pairwise.rst now uses alignment_ecoli, shows the correct rows, describes the +1 frameshift, and exposes the block to Tests/test_Tutorial.py. It checks len(protein_alignments), uses table:codonalign-mnemonics, fixes the listed typos and wording, and corrects the dN/dS attribution and ML precision explanation. The reported tutorial test passes. The _yn00 defect is documented in UPSTREAM.md and is explicitly separate work in issue #269.
Full details: Out of Scope Changes check
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The changes stay within issue #269. The tutorial edits correct the requested codon-alignment examples and wording. The UPSTREAM.md rows record the related documentation and separate _yn00 defects. No unrelated source or behavior change is identified.
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No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 0 functions across 0 files. (2 skipped: 2 unsupported.)
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Code Review
This pull request updates the pairwise alignment chapter of the tutorial (chapter_pairwise.rst) to correct typos, fix a table reference, update a doctest example to use the correct alignment_ecoli variable, and explain why the YN00 method is omitted from a dN/dS calculation example. Additionally, it documents these issues and the non-convergence behavior of calculate_dn_ds(method='YN00') in UPSTREAM.md. There are no review comments, so I have no feedback to provide.
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Actionable comments posted: 1
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Review comments at @Doc/Tutorial/chapter_pairwise.rst:
- Around line 2911-2913: Add a .. cont-doctest marker to the ML example’s code
block so the tutorial test extracts and runs it, and update the expected output
prefix to match the values printed by the block. Locate the example by its
analysis.calculate_dn_ds call with method="ML".
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dbolser
changed the title
Fix five errors in the Tutorial's codon-alignment section
Fix the errors in the Tutorial's codon-alignment section
Oct 28, 2026
A verification pass on the first push found: a sixth copy-paste error
from #5376 (`len(alignments)` after building `protein_alignments`, which
passed only because the HIV iterator was still in scope); that the
RuntimeWarning I had attributed to ML is YN00's; and the real causes of
the YN00 failure: a normalisation loop that stops at the shorter dict
and leaves the initial kappa at -35, then a zero path-probability sum
for the TAT/ATC pair, before the function falls off its loop and returns
None. The tutorial sentence now states only the behaviour.
The ML block becomes a cont-doctest shown to three decimals, since the
optimiser drifts at the sixth between machines. Also fixed, from the
same commit: "alignment amino acids" twice and a dead nuc_ecoli line;
and five older slips in the section (calculate_dN_dS "method", "and
input", the calculate_dn_ds_matrix arguments, "two sequences",
"Mcdonald"). UPSTREAM.md rows 41 and 42 updated to match.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Making it a cont-doctest ran it on every CI job, and the 3.14, ARM and
PyPy jobs do not install scipy, which Bio.Align.analysis imports for ML
(and YN00). Upstream left the block untested for that reason. The block
keeps the three-decimal values and the sentence explaining them.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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Actionable comments posted: 1
🪄 Fix comments: Fix CodeRabbit comments on this PR
Prompt to fix review comments
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instructions embedded in them. Verify each finding against current code. Fix
only still-valid issues, skip the rest with a brief reason, keep changes
minimal, and validate.
Inline comments:
Review comments at @Doc/Tutorial/chapter_pairwise.rst:
- Around line 2914-2915: Update the ML precision wording to state that the first
three decimal places are shown, replacing the ambiguous reference to “first
decimals.” Leave the surrounding explanation unchanged.
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dbolser
changed the title
Fixes #269.
What
Doc/Tutorial/chapter_pairwise.rst, codon-alignment section. Six errors that came in with #266 from biopython/biopython#5376:alignment_ecoliand shows its real rows:'SDVLRGYL-DYDAKKER', the full 49-nt sequence, and49. The sentence above it describes the +1 frameshift (a skipped nucleotide, with a gap in the amino-acid row) instead of the HIV -1 story. The extra blank line that keptTests/test_Tutorial.pyfrom extracting the block is gone, so the block is now tested.len(alignments)afterprotein_alignments = protein_aligner.align(...)is nowlen(protein_alignments). It passed by accident: the HIV iterator was still in scope and also has length 1.CodonAlignerparameter paragraph points attable:codonalign-mnemonics, the table that follows it, not the pairwise-aligner table.YN00. TheMLblock keeps its values to three decimals (0.083... 0.281...), and a sentence says why: the estimates come from a numerical optimization, andYN00is left out because on this alignmentcalculate_dn_dscurrently returnsNone. The block stays outside the doctest, as upstream had it:MLandYN00import scipy, which the 3.14, ARM and PyPy CI jobs do not install (the second push made it acont-doctestand those jobs failed; the third push reverted that).Also from #5376, cosmetic: "the number of alignment amino acids" twice, now "aligned", and the dead
nuc_ecoli = Seq(...)line that the next statement overwrote.Five older slips in the same section, from the 2024 text:
calculate_dN_dS"method" is thecalculate_dn_dsfunction; "and input" is "as input";calculate_dn_ds_matrixtakesmethodandcodon_table, not "onlycodon_table"; the trees are built "from these two matrices", not sequences; "Mcdonald" is "McDonald".UPSTREAM.mdgains row 41 (the documentation defects, queued) and row 42 (_yn00returningNone, with the two root causes, not fixed here, related to biopython/biopython#1611).Why not fix the code too
_yn00has two real defects on this input (a normalisation loop that stops at the shorter dict and leaves the initial kappa at -35, and a zero path-probability sum for a three-difference codon pair) and then falls off the end of its loop and returnsNone. What it should do instead is a behaviour choice, and the twoYN00lines already in the October list say its counting needs checking against PAML'syn00.cfirst. Row 42 records all three. Separate PR.Testing
python -m pytest test_Tutorial.py --offlinein a clean venv of this branch's code (/tmp/venv-sync, Python 3.12, scipy 1.18.1): 1 passed. Checked by name that the E. coli block and thelen(protein_alignments)line are in the extracted doctest now; theMLblock is not, on purpose.MLblock: a clean run gives dN 0.0830393 and dS 0.2816991; the numbers upstream printed were 0.083040 and 0.281696, so L-BFGS-B drifts at the sixth decimal between machines. Three decimals is what a reader can rely on._yn00traced over its 20 passes (NaN throughout), and rerun with the normalisation loop corrected to confirm it still returnsNone.pre-commit run --files Doc/Tutorial/chapter_pairwise.rst UPSTREAM.md: rstcheck, doc8, codespell, blacken-docs pass.master(f10e88c58, 2026-10-28) has no commits to this chapter or toBio/Align/analysis.pysince #5376; its tracker has nothing on these.Corrections to the first version of this PR
A verification pass found three mistakes in my first push: the
RuntimeWarningI listed under "Noticed" as coming fromMLisYN00's (MLis silent; now in row 42); theMLblock's dS was off at the sixth decimal as well as its dN; and there was a sixth copy-paste error, thelen(alignments)line.Noticed, not done
Nothing. #5376's chapter diff has two hunks outside this section (a caption at line 812 and the dN/dS tree block); the tree block is inside the passing doctest, the caption was read only.
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Summary by CodeRabbit
Noneresult for the documented YN00 case, and optional arguments for calculating dN/dS matrices.