NAME

bpy-subsample - Retain regularly spaced lines from a text stream.

SYNOPSIS

bpy-subsample [OPTIONS] [FACTOR] < INPUT > OUTPUT

DESCRIPTION

Read text from standard input and write selected lines to standard output. Use this to thin a table or a tree sample containing one tree per line. Blank lines count as lines; the tool does not recognize multiline records. Use cut-range for sampled alignments or other records marked by iteration values.

Selection proceeds in this order: preserve an optional header, skip initial data lines, subsample the remaining lines, and stop at the output limit. The first data line after skipping is always selected unless the output limit is zero.

ARGUMENTS AND OPTIONS

-h, --help

Print help and exit.

FACTOR

Optional positional subsampling factor. Default: 1. An integer factor N keeps data lines 1, 1+N, 1+2N, and so on after skipping. Fractional factors are allowed: 1.5 keeps lines 1, 3, 4, 6, 7, 9, and so on. The factor must be finite and positive. Factors below 1 keep every line.

--skip N

Discard the first N data lines, after any preserved header. Default: 0.

--max N

Maximum number of data lines to write. Omission means no limit; zero writes no data lines. A preserved header does not count toward this limit.

--header

Copy the first input line before applying selection to the remaining data lines. The header does not count toward --skip or --max. Empty input produces no output.

EXAMPLES

Keep the first tree and every tenth tree thereafter from a one-tree-per-line file:

bpy-subsample 10 < C1.trees > C1.thinned.trees

Preserve a table header, skip 100 data rows, then keep at most 500 rows spaced five rows apart:

bpy-subsample 5 --header --skip=100 --max=500 < C1.tsv > selected.tsv

EXIT STATUS

Returns 0 on success (including help) and 1 on an error.

SEE ALSO

cut-range(1), stats-cat(1), statreport(1)

REPORTING BUGS

BAli-Phy online help: https://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.