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refdb_clean_seq_crop_primers returns NA if one primer is not found:
repex:
primer_F <- paste0(rep("A",20), collapse = "") primer_R <- paste0(rep("T",20), collapse = "") SEQ <- paste0(rep("CG",10), collapse = "") seq_w_F <- paste0(primer_F, SEQ, collapse = "") seq_w_R <- paste0(SEQ, primer_R, collapse = "") seq_FR <- paste0(primer_F, SEQ, primer_R, collapse = "") test <- tibble(primer = c("seq_w_F", "seq_w_R", "seq_FR", "seq_noP"), sequence = c(seq_w_F, seq_w_R, seq_FR, SEQ)) %>% refdb_set_fields(sequence = "sequence") refdb_clean_seq_crop_primers(test, primer_F, primer_R, include_primers = F)
this results in
primer sequence <chr> <DNA> 1 seq_w_F NA 2 seq_w_R NA 3 seq_FR CGCGCGCGCGCGCGCGCGCG 4 seq_noP NA
I think it should default (or have the option) to crop the primers if they are found but to keep it if none or only one is found.
PS. I realize the the function is a wrapper for bioseq::seq_crop_pattern where this is the documented behavior...
bioseq::seq_crop_pattern
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refdb_clean_seq_crop_primers returns NA if one primer is not found:
repex:
this results in
I think it should default (or have the option) to crop the primers if they are found but to keep it if none or only one is found.
PS. I realize the the function is a wrapper for
bioseq::seq_crop_pattern
where this is the documented behavior...The text was updated successfully, but these errors were encountered: