cdskit printseq

cdskit printseq writes records whose sequence IDs fully match a regular expression to standard output.

Example

Command

cdskit printseq --seq_file input.fasta --seq_name_regex 'seq_[AG]' > output.fasta

input.fasta

>seq_A
AAAAAAAAAAAA
>seq_T
TTTTTTTTTTTT
>seq_G
GGGGGGGGGGGG
>seq_C
CCCCCCCCCCCC

output.fasta

>seq_A
AAAAAAAAAAAA
>seq_G
GGGGGGGGGGGG

Notes

• Matching uses the complete record ID. For substring matching, include .* explicitly, for example --seq_name_regex '.*kinase.*'.
• --show_seq_name no writes sequence strings without FASTA header lines.
• This command has no --out_file option; redirect standard output as shown above when a file is required.

Citation

No separate method paper is designated for this utility. Report the CDSKIT version, command and options; see citing CDSKIT.