cdskit rmseq

cdskit rmseq removes records whose IDs fully match a regular expression or whose sequences contain too many configured problematic characters.

Example

Command

cdskit rmseq --seq_file input.fasta --seq_name_regex "Arabidopsis_thaliana.*" --problematic_percent 50 --out_file output.fasta

input.fasta

>Aquilegia_coerulea_1
AGAGTTCAATATGCTTTGAGTCGAATTCGTAACAATGCTAGAAATCTTCTTACTCTTGAT
>Aquilegia_coerulea_2
AGAGTTCAATATGCTTTAAGTCGAATTCGAAACAATGCTAGAAATCTTCTCACTCTGGAT
>Aquilegia_coerulea_3
AGAGTTCAATATGCTTTAAGTCGAATTCGTAACAATGCAAGAAATCTTCTTACACTTGAT
>Hylocereus_undatus_1
AGGGTCCAATATGTTCTGAGCCGTATCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>Hylocereus_undatus_2
AGGGTTCAATACGTTCTGAGCCGTATCCGTAATGCTGCAAGGCATCTTCTTACCCTGGAT
>Hylocereus_undatus_3
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGCGGCAAGGCACCTTCTCACTCTGGAT
>Arabidopsis_thaliana_1
AGAGTTCAATATACACTTAGCAGAATCCGTAATGCTGCAAGAGAACTCTTAACTCTTGAT
>Arabidopsis_thaliana_2
AGAGTGCAGTACTCTCTTAGCCGTATCCGTAATGCTGCTAGAGATCTTTTGACTCTTGAT

output.fasta

>Aquilegia_coerulea_1
AGAGTTCAATATGCTTTGAGTCGAATTCGTAACAATGCTAGAAATCTTCTTACTCTTGAT
>Aquilegia_coerulea_2
AGAGTTCAATATGCTTTAAGTCGAATTCGAAACAATGCTAGAAATCTTCTCACTCTGGAT
>Aquilegia_coerulea_3
AGAGTTCAATATGCTTTAAGTCGAATTCGTAACAATGCAAGAAATCTTCTTACACTTGAT
>Hylocereus_undatus_2
AGGGTTCAATACGTTCTGAGCCGTATCCGTAATGCTGCAAGGCATCTTCTTACCCTGGAT

Key options

• --seq_name_regex REGEX removes complete-ID matches. Add .* around a substring when needed.
• --problematic_chars CHARS defines characters counted by --problematic_percent; the default is NX-? and matching is case-insensitive.
• --problematic_percent FLOAT removes a record when the configured characters occupy at least that percentage of its sequence. 0 disables this rule.

The ID and problematic-character rules are combined with OR: satisfying either rule removes the record.

Citation

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