split

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

or advanced expressions specified in the output path (-o/--output). See --help and --help-vars for more information. In contrast to other commands, the output argument (-o) of the 'split' command can contain variables/functions to determine the file path for each sequence.

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
(...)