Calculates the probability of a sequence, given a background model.
seq-proba [-i inputfile] [-o outputfile] [-v]
A sequence file, in any of the supported formats.
A tab-delimited file with one row per sequence, and two columns indicating (1) sequence ID; (2) sequence probability given the background model.
Level of verbosity (detail in the warning messages during execution)
Display full help message
Same as -h
If no input file is specified, the standard input is used. This allows to use the command within a pipe.
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.
Format of the background model. Supported: all input formats supported in convert-background-model.
List of fields to return (default: id,proba_b).
Supported fields: id,proba_b,len,seq
Probability of the sequence given the background model.
Complete detail of the computation with transition frequencies + the incremental computation of the probability. .
This should be relatively easy to implement.