shenwei356 / shenwei356/seqkit
[feature request] seqkit subseq with --circular option?
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- Go
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Description
Hi Wei,
I wonder would it be possible to add a --circular option also to seqkit subset?
I am currently using seqkit subset to extract the flanking regions of some genes with bed files. Some genes are located near the boundary of circular genomes so the flanks get truncated. It would be nice to have this option so that I don't need to manually concatenate the sequences multiple times before annotating genes. It would be even nicer if seqkit subset could differentiate linear/circular genomes with a user specified list or bed. For example:
seq_a linear
seq_b circular
...
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Research direction
Start by locating the seqkit subset command and reviewing how BED-defined flanking regions are extracted; compare the requested behavior with the existing seqkit subseq --circular option mentioned in the title. Define how circular versus linear sequences are selected, including the proposed sequence-name list or BED input, and verify that boundary-spanning flanks are extracted correctly.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- go
- Domain
- bioinformatics, cli
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 28/100