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Fix alignment filename assumptions #1206

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merged 4 commits into from
May 4, 2023
Merged

Fix alignment filename assumptions #1206

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b1b87dd
tests: tree: Add failing test with input alignment filename not endin…
tsibley May 4, 2023
39299c7
tree: Remove assumption that the input alignment filename ends in .fasta
tsibley May 4, 2023
f523a50
tree: Quote additional values we use to construct the IQ-TREE shell c…
tsibley May 4, 2023
7b77437
CHANGES: Document `augur tree` input alignment filename fix
tsibley May 4, 2023
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2 changes: 2 additions & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@

* filter, frequencies, refine, parse: Previously, ambiguous dates in the future had a limit of today's date imposed on the upper value but not the lower value. It is now imposed on the lower value as well. [#1171][] (@victorlin)
* refine: `--year-bounds` was ignored in versions 9.0.0 through 20.0.0. It now works. [#1136][] (@victorlin)
* tree: Input alignment filenames which do not end in `.fasta` are now properly handled when using IQ-TREE. Previously their contents were overwritten first by `augur tree` itself (resulting in truncation) and then by the log output of IQ-TREE (resulting in an error). Thanks to Jon Bråte for reporting this bug. [#1206][] (@tsibley)

[#728]: https://github.com/nextstrain/augur/pull/728
[#812]: https://github.com/nextstrain/augur/pull/812
Expand All @@ -32,6 +33,7 @@
[#1196]: https://github.com/nextstrain/augur/pull/1196
[#1200]: https://github.com/nextstrain/augur/pull/1200
[#1203]: https://github.com/nextstrain/augur/pull/1203
[#1206]: https://github.com/nextstrain/augur/pull/1206
[`pandas.read_csv()`]: https://pandas.pydata.org/pandas-docs/version/1.5/reference/api/pandas.read_csv.html

## 21.1.0 (14 March 2023)
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6 changes: 3 additions & 3 deletions augur/tree.py
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Expand Up @@ -246,8 +246,8 @@ def random_string(n):


# IQ-tree messes with taxon names. Hence remove offending characters, reinstaniate later
tmp_aln_file = aln_file.replace(".fasta", "-delim.fasta")
log_file = tmp_aln_file.replace(".fasta", ".iqtree.log")
tmp_aln_file = str(Path(aln_file).with_name(Path(aln_file).stem + "-delim.fasta"))
log_file = str(Path(tmp_aln_file).with_suffix(".iqtree.log"))
num_seqs = 0
with open(tmp_aln_file, 'w', encoding='utf-8') as ofile, open(aln_file, encoding='utf-8') as ifile:
for line in ifile:
Expand All @@ -264,7 +264,7 @@ def random_string(n):

if substitution_model.lower() != "auto":
call = [iqtree, "-ntmax", str(nthreads), "-s", shquote(tmp_aln_file),
"-m", substitution_model, tree_builder_args, ">", log_file]
"-m", shquote(substitution_model), tree_builder_args, ">", shquote(log_file)]
else:
call = [iqtree, "-ntmax", str(nthreads), "-s", shquote(tmp_aln_file), tree_builder_args, ">", shquote(log_file)]

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11 changes: 11 additions & 0 deletions tests/functional/tree.t
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Expand Up @@ -53,6 +53,17 @@ Since the following custom arguments are incompatible with the default IQ-TREE a
> --override-default-args \
> --output "$TMP/tree_raw.nwk" > /dev/null

Build a tree with an input file that doesn't end in .fasta, and ensure it's not overwritten.

$ ${AUGUR} tree \
> --alignment tree/aligned.fa \
> --method iqtree \
> --output "$TMP/tree_raw.nwk" \
> --nthreads 1 > /dev/null

$ sha256sum tree/aligned.fa
169a9f5f70b94e26a2c4ab2b3180d4b463112581438515557a9797adc834863d tree/aligned.fa

Clean up tree log files.

$ rm -f tree/*.log
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