split

Distribute sequences into multiple files based on a variable/function or advanced expression

In contrast to other commands, the output argument (-o/--output) of the 'split' command can contain variables and advanced expressions to determine the file path for each sequence. However, the output format will not be automatically determined from file extensions containing variables.

Usage: st split [OPTIONS] [INPUT]...

Options:
  -h, --help  Print help

'Split' command options:
  -n, --num-seqs <N>     Split into chunks of <N> sequences and writes each
                         chunk to a separate file with a numbered suffix. The
                         output path is: '{filestem}_{chunk}.{default_ext}',
                         e.g. 'input_name_1.fasta'. Change with `-o/--output`
  -p, --parents          Automatically create all parent directories of the
                         output path
  -c, --counts <COUNTS>  Write a tab-separated list of file path + record count
                         to the given file (or STDOUT if `-` is specified)

See this page for the options common to all commands.

Immagine this FASTA file (input.fa):

>seq1 group=1
SEQUENCE
>seq2 group=2
SEQUENCE
>seq3 group=1
SEQUENCE

st split -o "group_{attr(group)}.fa" input.fasta

This will create the files group_1.fa and group_2.fa. In more complicated scenarios, variables may be combined for creating nested subfolders of any complexity.

An example of de-multiplexing sequences by forward primer is found in the documetation of the find command.

Variables available in the split command

chunk	If -n/--num-seqs was specified, the 'chunk' variable contains the number of the current sequence batch, starting with 1. Note that the 'chunk' variable is only available with -n/--num-seqs, otherwise there will be a message: "Unknown variable/function: chunk"

Example

Split input into chunks of 1000 sequences, which will be named outdir/file_1.fq, outdir/file_2.fq, etc.:

st split -n 1000 -po 'outdir/out_{chunk}.fq' input.fastq

Output files (`ls outdir/out_*.fq`):
outdir/out_1.fq
outdir/out_2.fq
(...)