Using Pred2ary from the command line

This version of Pred2ary can be run interactively as well as non-interactively. The latter mode is most useful for processing a lot of proteins in batch.

Pred2ary has the following syntax:

java pred2ary [-?] [--] [-help] [-file] networks -p prediction_protein_file
              [-op prediction_output_file] [-o output_file]
              [-combine] [-choose N] [-blastlocal] [-blast] [-blastnet URL]
              [-psiblastlocal] [-psiblast] [-psiblastnet URL]  

  Run with no options to get the interactive version.

  -?, --, or -help - describes all the options
  -pr - prediction set (readable protein or profile format)
        (here's a description of possible formats.)
  -op - prediction set output file (EA format, by default)
     YAPF, PDB, CASP3 format can be specified by file suffix (i.e. x.yapf)
  -o  - output file [stdout]
  -file - means the jury of networks is in a file in your computer.
          (rather than one included in the package)
  -combine - combine all proteins in input file into 1 profile.
             (for loading a profile stored in a bunch of FASTA files)
  -choose N - choose the n'th sequence in each profile, starting at 0.
              (same effect as clicking on the n'th sequence)
  -blastlocal - run BLAST (locally, using 'blastall') on each protein.
  -blast - run BLAST (over net, at NCBI) on each protein.
  -blastnet URL - run BLAST (over net, at some URL) on each protein.
  -psiblastlocal - run PSI-BLAST (locally, using 'blastpgp') on each protein.
  -psiblast - run PSI-BLAST (over net, at NCBI) on each protein.
  -psiblastnet URL - run PSI-BLAST (over net, at some URL) on each protein.
 
  networks can be 'small', 'medium', or 'large',
    or in a user-specified file, if you use the -file option.
    (here's a description of the included juries)