cdskit aggregate

cdskit aggregate groups sequence IDs after removing one or more regular expression matches, then retains the longest sequence in each group. The original ID of the retained record is preserved.

Example

Command

cdskit aggregate --seq_file input.fasta --out_file 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

Notes

• Values passed to --expression are applied sequentially. In this example, :.* and \|.* reduce the IDs to the group keys seq1 and seq2.
• --mode longest is currently the only selection mode. Ties retain the first record encountered in the input.
• If --expression is omitted, records are copied without aggregation.

Citation

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