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Move accession to the first column of metadata_all.tsv #36

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merged 2 commits into from
Feb 24, 2024
Merged

Move accession to the first column of metadata_all.tsv #36

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b68a6aa
Move accession to the first column of metadata_all.tsv
j23414 Feb 23, 2024
3631e90
Document the notable columns in merging USVI and GenBank data
j23414 Feb 23, 2024
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9 changes: 8 additions & 1 deletion phylogenetic/rules/merge_sequences_usvi.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,13 @@ This part of the workflow usually includes the following steps:
"""

rule append_usvi:
"""Appending USVI sequences"""
"""Appending USVI sequences

Notable columns:
- accession: Either the GenBank accession or USVI accession.
- genbank_accession: GenBank accession for Auspice to generate a URL to the NCBI GenBank record. Empty for USVI sequences.
- url: URL used in Auspice, to either link to the USVI github repo (https://github.com/blab/zika-usvi/) or link to the NCBI GenBank record ('https://www.ncbi.nlm.nih.gov/nuccore/*')
"""
input:
sequences = "data/sequences.fasta",
metadata = "data/metadata.tsv",
Expand All @@ -43,5 +49,6 @@ rule append_usvi:
-n accession \
-e '$genbank_accession' \
| csvtk concat -tl - {input.usvi_metadata} \
| tsv-select -H -f accession --rest last \
Comment on lines 51 to +52
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(non-blocking)

Suggestion: In cases like this where a column name is ambiguous, add more detail somewhere in the repo. Maybe as the docstring of this rule:

rule append_usvi:
    """Appending USVI sequences.

    Notable columns:
    - accession: Either the GenBank accession or USVI accession.
    - genbank_accession: For Auspice to generate a URL to the NCBI GenBank record. Empty for USVI sequences.
    - url: ?
    """
    input:
        …

I don't know if this has been done in other repos, but it seems like it'd be useful to bring this context out of commit messages/PRs and into the code itself.

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@j23414 j23414 Feb 23, 2024 •
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Thanks, agree with writing the context into the code itself (docstring). Fixed with 3631e90 but let me know if the url explanation is confusing

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(Discussion is beyond the scope of this PR now, so feel free to merge first.)

The Auspice source code indicates that when both are specified, genbank_accession takes precedence and url will be ignored.

Because of this behavior, I don't think url should be set for GenBank sequences. That would only cause confusion in the event that GenBank changes the URL, we try to update it in this file, and scratch our heads over why the old URL is still showing on Auspice. I would expect url to only be set for USVI sequences where there is no genbank_accession.

> {output.metadata}
"""