merge: Support sequences with cross-checking #1601
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1601 +/- ##
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+ Coverage 72.24% 72.51% +0.27%
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Files 79 79
Lines 8268 8459 +191
Branches 1691 1731 +40
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+ Hits 5973 6134 +161
- Misses 2009 2027 +18
- Partials 286 298 +12 ☔ View full report in Codecov by Sentry. |
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--sequences + --output-sequences--sequences + --output-sequences with cross-checking
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--sequences + --output-sequences with cross-checking
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Preparing for use across functions.
Preparing for use across functions.
Preparing for use across functions.
Preparing for NamedSequences
Preparing for sequence support.
Sequence support will require the ability to load metadata into the database without actually merging (if --output-metadata is not specified).
Preparing for sequence support, which allows unnamed inputs.
Add sequence support in addition to the existing metadata support. SeqKit is used to deduplicate across sequence files. Duplicates within an individual sequence file are not supported. Those are checked by reading IDs using read_sequences.
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@tsibley this is ready for initial review whenever you get the chance! |
genehack
reviewed
Oct 24, 2024
| def run(args): | ||
| print_info = print_err if not args.quiet else lambda *_: None | ||
| def validate_arguments(args): | ||
| # These will make more sense when sequence support is added. |
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comment can go away, as this is adding sequence support?
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| def load_metadata( | ||
| db: Database, | ||
| metadata: List[NamedMetadata], | ||
| ): |
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Suggested change
| def load_metadata( | |
| db: Database, | |
| metadata: List[NamedMetadata], | |
| ): | |
| def load_metadata( | |
| db: Database, | |
| metadata: List[NamedMetadata], | |
| ) -> List[NamedMetadata]: |
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| # Confirm that seqkit is installed. | ||
| if which("seqkit") is None: | ||
| raise AugurError("'seqkit' is not installed! This is required to merge sequences.") |
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This duplicates a check that's also done on L717; that latter check is also looking at the SEQKIT env var, which this check isn't.
I'm not sure which one is correct, but it doesn't seem like both are useful?
This was referenced Dec 4, 2024
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| $ source "$TESTDIR"/_setup.sh | ||
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| BASIC USAGE |
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🐛 at 81b22d7. when a FASTA doesn't have a trailing new line it results in a malformed merged FASTA.
e.g. 2 fasta files each without trailing new lines:
# A.fasta
>A
ATGC
# B.fasta
>B
ATGC
$ augur merge --sequences A=A.fasta B=B.fasta --output-sequences -
>B
ATGC>AATGCI also find it strange that B comes before A in the output - is this on purpose?
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Description of proposed changes
Initial prototype for sequence support in
augur mergewhere metadata and sequence merge happens with additional cross-checking.Related issue(s)
Closes #1579
Checklist