NAME

cut-range - Select complete records by their logged key values.

SYNOPSIS

cut-range [OPTIONS] [FILE ...]

DESCRIPTION

Select records from text files using a numeric key, usually the iteration number recorded with each sampled alignment. Each marker line and the following lines, up to the next marker, form one record. Selected records are copied to standard output in input-file order.

The default marker contains the exact text iterations =, followed by a number. The spaces around = matter; the marker need not begin the line. --key changes the key name. Key values must be in ascending order: reading a file stops at the first value above the upper bound.

Bounds and subsampling apply independently to every file. Text before the first marker is copied when --skip is omitted and discarded when it is supplied. With no filenames, read standard input; - also denotes standard input.

OPTIONS

-h, --help

Print help and exit.

--key NAME

Select using markers containing NAME = followed by a number. Default: iterations.

--skip N

Minimum key value to retain, inclusive. By default, there is no lower bound. This is a key-value cutoff, not a number of records to discard.

--until N

Maximum key value to retain, inclusive. By default, there is no upper bound.

--size N

Key-value span to retain. The inclusive upper bound is skip + N, using zero when --skip is omitted. For example, --skip=100 --size=20 retains keys from 100 through 120. This limits the range of key values, not the number of records. Cannot be combined with --until.

--subsample N

Keep the first eligible record and every Nth eligible record thereafter, restarting for each file. N must be at least 1. Default: 1.

--verbose

Write additional diagnostic messages to standard error.

EXAMPLES

Select sampled alignments with iteration values from 100 through 1000:

cut-range --skip=100 --until=1000 run-1/C1.P1.fastas > selected.fastas

From each of two runs, retain every tenth eligible alignment starting at iteration 100:

cut-range --skip=100 --subsample=10 run-1/C1.P1.fastas run-2/C1.P1.fastas > pooled.fastas

EXIT STATUS

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

SEE ALSO

bpy-subsample(1), alignment-chop-internal(1), alignment-max(1)

REPORTING BUGS

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

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