Generate gene reference files #47
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This is a fixup to an earlier commit: 8cd6a13 This updates the docs to reflect that the script will NOT just throw a warning, but actually error out if the gene is not found in the GenBank file. This was flagged by comment: nextstrain/dengue#47 (comment)
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I was wondering why the CI was taking so long, then remembered that example files gets connected to "phylogenetic/data" Fixed with: 30b1d5a |
https://github.com/nextstrain/rsv/blob/a1788ce2c9c4375fb5a06d1426c64c45cf90225f/scripts/newreference.py fixup: fix comments to match behavior Co-authored-by: John SJ Anderson <[email protected]>
Adds some wildcard constraints on serotype-gene combinations to avoid
unchecked wildcard matching, such as having {serotype}.fasta match both
"denv1_E.fasta" and "denv1.fasta".
This is in preperation of having separate genome and gene (e.g. E, NS1) reference files.
This is in preperation of nesting each gene's specific files in subdirectories (e.g. `results/E/tree.nwk`) as suggested in comment: * nextstrain/private#102 (comment)
In prep of building "genome" and "E" intermediate and final files for the phylogenetic pipeline.
Move gene annotation to top of CDS to match other genbank files (denv1,3,4)
This generates the reference_serotype_gene.gb and reference_serotype_gene.fasta files for each serotype. These files can then be subsequently used in augur align, augur translate, and optionally for nextclade align during the gene trees.
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This is a fixup to an earlier commit: 8cd6a13 This updates the docs to reflect that the script will NOT just throw a warning, but actually error out if the gene is not found in the GenBank file. This was flagged by comment: nextstrain/dengue#47 (comment)
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Description of proposed changes
In order to support gene phylogenetic trees (e.g. E gene trees), add rules to automatically generate gene reference GenBank and FASTA files (e.g.
reference_denv4_E.gbandreference_denv4_E.fasta) by following the rules used in RSV.This is part of a larger and older issue of creating E gene builds and is being split out into smaller PRs to maintain QC and scope of review. This will not generate an E gene phylogenetic tree, subsequent PRs will modify this to generate the trees.
Visual summary (view whole pipeline plan so far)
Related issue(s)
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Example shortened reference_denv2_E.gb