Skip to content

cdskit aggregate

Jump to bottom
Kenji Fukushima edited this page Mar 6, 2023 · 3 revisions

cdskit aggregate extracts the longest sequences combined with a sequence name regex.

Example

Command

cdskit aggregate --seqfile input.fasta --outfile output.fasta --expression ":.*" "\|.*"

input.fasta

>seq1:1.length=30nt
ATGCTAAGCGGTAATCTAAGCGGTAATTGA
>seq1:2.length=27nt
ATGCTAAGCGGTAATCTAAGCGGTTGA
>seq1:3.length=33nt
ATGCAACTAAGCGGTAATCTAAGCGGTAATTGA
>seq2|1.length=45nt
ATGTCGGAATTGCGAGTAAGCACCAGCTTCTCAAAACCAAAATAA
>seq2|2.length=54nt
ATGTCGAGATCCCGAGAATTGCGAGTAAGCACCAGCTTCTCAAAACCAAAATAA

output.fasta

>seq1:3.length=33nt
ATGCAACTAAGCGGTAATCTAAGCGGTAATTGA
>seq2|2.length=54nt
ATGTCGAGATCCCGAGAATTGCGAGTAAGCACCAGCTTCTCAAAACCAAAATAA

Clone this wiki locally