NAME¶

pbsEncode - Produce an approximate binary encoding of a probabilistic

DESCRIPTION¶

Produce an approximate binary encoding of a probabilistic biological sequence (PBS), as defined by a text file ("input.probs") with a row for each position in the sequence and a column for each base. The (i,j)th value in this table should be the probability of base j at position i. Columns should be white-space delimited. The encoding will be as defined by "codefile", which should be in the format used by pbsTrain.

This program performs the inverse function of pbsDecode.

EXAMPLE¶

Encode the probabilities in a file "anc.human-mouse.probs", produced by prequel, using a code file "mammals.code", produced by pbsTrain. pbsEncode anc.human-mouse.probs mammals.code > anc.human-mouse.bin

OPTIONS¶

--discard-gaps, -G

Discard gaps in the PBS.

Gaps in the input data are assumed

to be represented by rows consisting of a single "-" character.

--help, -h Produce this help message.