- edited description
Additional features to add to ConvertDb-genbank
-
Add a flag to ConvertDb-genbank to retain invalid CDS (stop codon) records, but convert the JUNCTION annotation to a
misc_feature
. -
Add arguments for
sex
andtissue-type
specification. -
AIRR formats support.
Comments (10)
-
reporter -
reporter - Add
COORDINATES
type to inference qualifiers. - Use
protein motif
for inference qualifier in CDS (JUNCTION) andalignment
for V, D, J and C segments.
- Add
-
reporter All of the above is done, except AIRR format support.
Also updated keywords to
TLS; Targeted Locus Study; AIRR; MiAIRR:1.0
. -
reporter We could probably add the execution of
tbl2asn
as an optional post-processing step as well. It should only require adding:- Input of a template
.sbt
file generated via https://submit.ncbi.nlm.nih.gov/genbank/template/submission. - Arguments for BioProject and BioSample accession numbers.
- An
--exec
argument to point totbl2asn
- A flag specifying whether or not to perform the step (
--asn
).
- Input of a template
-
reporter AIRR format support added in 35caac8. At the time of writing, this is dependent upon the version of the AIRR standard in the Rearrangement-fields branch.
-
reporter Could use a small vignette/tutorial for this in the changeo docs.
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reporter Added support for non-IMGT gene names and AIRR_READ_COUNT and AIRR_CELL_INDEX notes in 353afd1.
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reporter Need to add support for passing all these various arguments via a yaml file instead of individually.
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reporter YAML config argument done in c6e6b1e.
-
reporter - changed status to resolved
tbl2asn execution added in af1ac5b.
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