Compute Gc Content

Input parsing and validation controls:

• --format {raw,fasta}

  • raw: treat the input as a plain sequence (whitespace ignored).
  • fasta: parse FASTA records (lines starting with ">" start new records).

• --strict

  • If set, error on invalid characters (anything other than A/C/G/T/N, ignoring whitespace).

• --ignore-ambiguous

  • If set, compute GC fraction over only A/C/G/T bases (exclude N and other ambiguous bases from the denominator).

Output control:

• --output {json,text}
  • Select JSON (machine-readable) or text output.

Output

• stdout:

  • Normal results. With --output json, emits a JSON object containing per-record results and an aggregate summary.

• stderr:

  • Errors (for example, invalid characters when --strict is enabled, missing inputs, or unsupported options).

Example stdout (JSON) for:

python scripts/compute_gc_content.py --sequence ACGTNNGCGC --output json

{ "results": [ { "header": null, "sequence_index": 0, "length": 10, "gc_fraction": 0.6 } ], "summary": { "records": 1, "total_length": 10, "mean_gc_fraction": 0.6 } }

When to use

Use when:

• You need GC fraction for one or more DNA sequences.
• You want to parse FASTA input and compute GC per record.
• You want optional strict validation and/or to exclude ambiguous bases from the denominator.

Do not use when:

• You need GC content for RNA (U) without pre-converting to DNA bases.
• You need sliding-window GC, per-position tracks, or other advanced sequence statistics not supported by this CLI.
• Your inputs include IUPAC ambiguity codes beyond N and you require them to be handled in a specific way (other than excluding them with --ignore-ambiguous).