
                             substituterunner 



Function

   Run SUBSTITUTE on a directory of traces

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
  [-alignedpairsdir]   dirlist    Directory containing paired traces
  [-substitutedseqsoutdir] outdir     Directory to write substituted sequences
to

   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
   [-alignedpairsdir]
   (Parameter 2) Directory containing paired traces Directory with files
   .
   [-substitutedseqsoutdir]
   (Parameter 3) Directory to write substituted sequences to Output
   directory
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   substituterunner reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   substituterunner 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
   scorerrunner   SCORER for ordered pairs of substituted seqs
   stretcher      Finds the best global alignment between two sequences
   substitute     Substitute matches into a template

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
