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Fix silent parse bug #1712

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merged 3 commits into from
Jan 14, 2025
Merged

Fix silent parse bug #1712

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5af78c4
parse: Add invalid characters to test data
huddlej Jan 8, 2025
a213d3a
parse: Transform strain name in the metadata
huddlej Jan 8, 2025
a4c79c2
Note bug fix in changelog
huddlej Jan 14, 2025
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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -16,10 +16,12 @@
* `augur curate rename --field-map`
* `augur curate transform-strain-name --backup-fields`
* `augur curate format-dates --expected-date-formats` help text has been improved with clarifications regarding how values provided interact with builtin formats and how to match masked date parts. [#1707][], [#1718][] (@victorlin)
* parse: Transform strain names the same way in both metadata and sequences instead of only transforming sequences. [#1712][] (@huddlej)

[#1688]: https://github.com/nextstrain/augur/pull/1688
[#1690]: https://github.com/nextstrain/augur/pull/1690
[#1707]: https://github.com/nextstrain/augur/issues/1707
[#1712]: https://github.com/nextstrain/augur/pull/1712
[#1715]: https://github.com/nextstrain/augur/pull/1715
[#1716]: https://github.com/nextstrain/augur/pull/1716
[#1718]: https://github.com/nextstrain/augur/pull/1718
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4 changes: 2 additions & 2 deletions augur/parse.py
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Expand Up @@ -138,8 +138,8 @@ def parse_sequence(
sequence_fields = map(str.strip, sequence.description.split(separator))
metadata = dict(zip(fields, sequence_fields))

tmp_name = metadata[strain_key].translate(forbidden_characters)
sequence.name = sequence.id = tmp_name
metadata[strain_key] = metadata[strain_key].translate(forbidden_characters)
sequence.name = sequence.id = metadata[strain_key]
sequence.description = ''

if prettify_fields:
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2 changes: 1 addition & 1 deletion tests/functional/parse.t
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Expand Up @@ -45,7 +45,7 @@ Parse Zika sequences into sequences and metadata using a different metadata fiel
> --fix-dates monthfirst

$ diff -u "parse/sequences_other.fasta" "$TMP/sequences.fasta"
$ diff -u "parse/metadata.tsv" "$TMP/metadata.tsv"
$ diff -u "parse/metadata_other.tsv" "$TMP/metadata.tsv"
$ rm -f "$TMP/sequences.fasta" "$TMP/metadata.tsv"

Try to parse Zika sequences with a misspelled field.
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13 changes: 13 additions & 0 deletions tests/functional/parse/metadata_other.tsv
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@@ -0,0 +1,13 @@
strain virus accession date region country division city db segment authors url title journal paper_url
PAN/CDC_259359( V1 )V3/2015 zika KX156774 2015-12-18 North America Panama Panama Panama genbank genome Shabman et al https://www.ncbi.nlm.nih.gov/nuccore/KX156774 Direct Submission Submitted (29-APR-2016) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/
COL/FLR_00024/2015 zika MF574569 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574569 Direct Submission Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/
PRVABC59 zika KU501215 2015-12-XX North America Puerto Rico Puerto Rico Puerto Rico genbank genome Lanciotti et al https://www.ncbi.nlm.nih.gov/nuccore/KU501215 Phylogeny of Zika Virus in Western Hemisphere, 2015 Emerging Infect. Dis. 22 (5), 933-935 (2016) https://www.ncbi.nlm.nih.gov/pubmed/27088323
COL/FLR_00008/2015 zika MF574562 2015-12-XX South America Colombia Colombia Colombia genbank genome Pickett et al https://www.ncbi.nlm.nih.gov/nuccore/MF574562 Direct Submission Submitted (28-JUL-2017) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/
Colombia/2016/ZC204Se zika KY317939 2016-01-06 South America Colombia Colombia Colombia genbank genome Quick et al https://www.ncbi.nlm.nih.gov/nuccore/KY317939 Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples Nat Protoc 12 (6), 1261-1276 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538739
ZKC2/2016 zika KX253996 2016-02-16 Oceania American Samoa American Samoa American Samoa genbank genome Wu et al https://www.ncbi.nlm.nih.gov/nuccore/KX253996 Direct Submission Submitted (18-MAY-2016) Center for Diseases Control and Prevention of Guangdong Province; National Institute of Viral Disease Control and Prevention, China https://www.ncbi.nlm.nih.gov/pubmed/
VEN/UF_1/2016 zika KX702400 2016-03-25 South America Venezuela Venezuela Venezuela genbank genome Blohm et al https://www.ncbi.nlm.nih.gov/nuccore/KX702400 Complete Genome Sequences of Identical Zika virus Isolates in a Nursing Mother and Her Infant Genome Announc 5 (17), e00231-17 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28450510
DOM/2016/BB_0059 zika KY785425 2016-04-04 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785425 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734
BRA/2016/FC_6706 zika KY785433 2016-04-08 South America Brazil Brazil Brazil genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785433 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734
DOM/2016/BB_0183 zika KY785420 2016-04-18 North America Dominican Republic Dominican Republic Dominican Republic genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785420 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734
EcEs062_16 zika KX879603 2016-04-XX South America Ecuador Ecuador Ecuador genbank genome Marquez et al https://www.ncbi.nlm.nih.gov/nuccore/KX879603 First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador Genome Announc 5 (8), e01673-16 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28232448
HND/2016/HU_ME59 zika KY785418 2016-05-13 North America Honduras Honduras Honduras genbank genome Metsky et al https://www.ncbi.nlm.nih.gov/nuccore/KY785418 Zika virus evolution and spread in the Americas Nature 546 (7658), 411-415 (2017) https://www.ncbi.nlm.nih.gov/pubmed/28538734
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