cdskit validate

cdskit validate runs basic quality checks for CDS alignments and prints a summary.

Example

Command

cdskit validate --seq_file alignment.fasta --codon_table 1 --report validate.json

What is checked

• Whether all sequence lengths are identical (aligned).
• Sequence lengths that are not multiples of three.
• Duplicate sequence IDs.
• Gap-only sequences.
• Sequences containing internal stop codons.
• Ambiguous codons and ambiguous-codon rate.

Key options

• --codon_table INT: NCBI codon table ID used for internal stop checks.
• --report PATH: Optional output report path (.json or tab-separated text). No report file is produced unless this option is specified. Use --report - to write only the TSV report to standard output (CDSKIT >=0.31.7).

TSV report format

TSV reports use schema version 2 and begin with schema_version and section. summary rows contain counts and rates; id_set rows contain compact JSON arrays for each category of affected sequence IDs.

Notes

• Without --report -, the human-readable summary is printed to standard output, including when saving a report to a named file. Successful reporting exits with status 0 even when QC issues are found; inspect the report fields to decide whether an alignment meets your criteria.
• --report - suppresses the human-readable summary so stdout contains one rectangular TSV. Runtime logs remain on stderr. In versions through 0.31.6, this option mixed the summary and TSV; use a named report file on those versions.
• ambiguous_codon_rate is a 0–1 ratio: ambiguous complete codons divided by evaluable complete codons (excluding codons with -, ?, or .). A zero denominator reports 0. gap_only_ids also includes all-N/all-X sequences, not just literal dashes.
• This command does not modify input sequences.

Codon semantics

See codon meaning and uncertainty for definite versus possible stops, dual-coding tables 27/28/31, overlapping ambiguity/stop counts, and report compatibility. These rules describe sequence QC, not gene function.

Citation

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