Subcommand: chunkify

Chunkify a set of fasta files and create abundance maps.

Usage: gappa prepare chunkify [options]

Options

Sequence Input
--fasta-path	Required. TEXT ... List of fasta files or directories to process. For directories, only files with the extension .(fasta|fas|fsa|fna|ffn|faa|frn) are processed.
Options
--chunk-size	UINT=50000 Number of sequences per chunk file.
--min-abundance	UINT=1 Minimum abundance of a single sequence. Sequences below are filtered out.
--hash-function	TEXT in {MD5,SHA1,SHA256}=SHA1 Hash function for re-naming and identifying sequences.
Output
--chunks-out-dir	TEXT=. Directory to write chunks files to
--chunk-file-prefix	TEXT=chunk_ File prefix for chunk files
--abundances-out-dir	TEXT=. Directory to write abundances files to
--abundance-file-prefix	TEXT=abundances_ File prefix for abundance files

Description