gp_randseq - generate random DNA sequences from a master sequence
gp_randseq [-l length] [-number] [-q] [-v] [-d] [-h] [inputfile] [outputfile]
- -n value
- set the number of random sequences to value
- -l value
- set the random sequence length to value
- instead of cutting out sequences at random positions in the
genome, computate the Markov chain probabilities for nucleotides
and generate sequences basing on that.
- Prints the version information.
- Prints lots of debugging information.
- Shows usage information.
- file to proces; if not given, will use standard input
- file to write the data to; if not given, will
use standard output
gp_randseq cuts out random sequences from a larger sequence. It is
useful in genomic comparisons (e.g. what will be the distribution
of a certain parameter in my set of sequences as compared to random
sequences). The probability distribution of the sequence start
should be linear.
All Genpak programs complain in situations you would also complain,
like when they cannot find a sequence you gave them or the sequence is not
The Genpak programs do not write over existing files. I have found this
feature very useful :-)
I'm sure there are plenty left, so please mail me if you find them. I tried
to clean up every bug I could find.
January Weiner III