NAME

seq-proba

DESCRIPTION

Calculates the probability of a sequence, given a background model.

AUTHORS

Jacques.van-Helden\@univ-amu.fr

CATEGORY

util

USAGE

seq-proba [-i inputfile] [-o outputfile] [-v]

INPUT FORMAT

A sequence file, in any of the supported formats.

OUTPUT FORMAT

A tab-delimited file with one row per sequence, and two columns indicating (1) sequence ID; (2) sequence probability given the background model.

OPTIONS

-v #

Level of verbosity (detail in the warning messages during execution)

-h

Display full help message

-help

Same as -h

-i inputfile

If no input file is specified, the standard input is used. This allows to use the command within a pipe.

-seq_format seq_format

Sequence format.

-bgfile background_file

Background model file.

This argument can be used iteratively to speciy alternative backgound models. In this case, the program returns the probabilities corresponding to each model in separate columns.

-bg_format bg_format

Format of the background model. Supported: all input formats supported in convert-background-model.

-return return_fields

List of fields to return (default: id,proba_b).

Supported fields: id,proba_b,len,seq

id

Sequence identifier.

proba_b

Probability of the sequence given the background model.

len

Sequence length.

seq

Sequence.

detail

Complete detail of the computation with transition frequencies + the incremental computation of the probability. .

SEE ALSO

convert-background-model

matrix-scan

WISH LIST

Support sequences with IUPAC letters

This should be relatively easy to implement.

For information, contact