
                               scorerrunner 



Function

   SCORER for ordered pairs of substituted seqs

Description

   **************** EDIT HERE ****************

Algorithm

   **************** EDIT HERE ****************

Usage

   Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-commandpath]       directory  Directory where alignment executables live
  [-goldseqsdir]       dirlist    First directory containing paired traces
  [-testseqsdir]       dirlist    Second directory containing paired traces
  [-scoresoutdir]      outdir     Name of directory containing output scores
  [-scoresoutfilename] string     Name of comma-separated variable file
                                  containing identity scores for pairs of gold
                                  and test sequences directory

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-commandpath]
   (Parameter 1) Directory where alignment executables live Directory
   [-goldseqsdir]
   (Parameter 2) First directory containing paired traces Directory with
   files .
   [-testseqsdir]
   (Parameter 3) Second directory containing paired traces Directory with
   files .
   [-scoresoutdir]
   (Parameter 4) Name of directory containing output scores Output
   directory
   [-scoresoutfilename]
   (Parameter 5) Name of comma-separated variable file containing
   identity scores for pairs of gold and test sequences directory Any
   string is accepted scores.csv
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   scorerrunner reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   scorerrunner outputs a graph to the specified graphics device. outputs
   a report format file. The default format is ...

   Under development, no example output file(s) yet

Data files

   **************** EDIT HERE ****************

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

     Program name                         Description
   alignrunner      Align sequence pairs in a directory
   comparator       Compare contact scores of two sequence alignments
   contactalign     Damian Counsell's experimental 2.5-D alignment algorithm
   esim4            Align an mRNA to a genomic DNA sequence
   est2genome       Align EST and genomic DNA sequences
   nawalign         Damian Counsell's NW implementation
   nawalignrunner   Nawalign all sequence pairs in a directory
   needle           Needleman-Wunsch global alignment
   needlerunner     Needle all sequence pairs in a directory
   scorer           Score alignments using structural alignments
   stretcher        Finds the best global alignment between two sequences
   substitute       Substitute matches into a template
   substituterunner Run SUBSTITUTE on a directory of traces

Author(s)

   Damian Counsell (d.counsell © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
