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Fastx Calc

Summary

Calculate per-sequence metrics (length, GC content, hash, etc.).

Description

This command computes metrics for each sequence in a FASTA/FASTQ file. For aggregate statistics across all sequences, use the 'fastx-stats' command instead.

Note: - No support yet for reverse complement (not in circular or hash).

Usage

rolypoly fastx-calc [OPTIONS]

Options

  • -i, --input: Input file (fasta, fa, fna, faa) (type: PATH; required; default: Sentinel.UNSET)
  • -o, --output: Output path (use 'stdout' to print to console) (type: PATH; default: rp_sequence_calc.tsv)
  • --format: Output format for per-sequence annotations (type: CHOICE; default: tsv)
  • -f, --fields: Fields to annotate for each sequence. Available: length - sequence length gc_content - percentage of GC nucleotides n_count - total number of Ns hash - md5 hash of the sequence (type: CHOICE; default: length, gc_content, n_count)
  • -c, --circular: Treat sequences as circular (rotate to minimal lexicographical form before hashing) (type: BOOLEAN; default: False)