Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

read_seqs for gbk splits LOCUS lines wrong #203

Open
thackl opened this issue Oct 18, 2024 · 0 comments
Open

read_seqs for gbk splits LOCUS lines wrong #203

thackl opened this issue Oct 18, 2024 · 0 comments

Comments

@thackl
Copy link
Owner

thackl commented Oct 18, 2024

When parsing gbk files for sequence length, the "LOCUS" line is split not just on white space, but any non-alphanumeric character. I.e. "LOCUS scaffold_20 50000 bp ..." gives seq_id="scaffold", length=20...

tidyr::separate(.data$raw, into = c("tag", "seq_id", "length"), extra = "drop", convert = TRUE) %>%

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant