scorerrunner

 

Function

SCORER for ordered pairs of substituted seqs

Description

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

Algorithm

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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

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Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
alignrunnerAlign sequence pairs in a directory
comparatorCompare contact scores of two sequence alignments
contactalignDamian Counsell's experimental 2.5-D alignment algorithm
esim4Align an mRNA to a genomic DNA sequence
est2genomeAlign EST and genomic DNA sequences
nawalignDamian Counsell's NW implementation
nawalignrunnerNawalign all sequence pairs in a directory
needleNeedleman-Wunsch global alignment
needlerunnerNeedle all sequence pairs in a directory
scorerScore alignments using structural alignments
stretcherFinds the best global alignment between two sequences
substituteSubstitute matches into a template
substituterunnerRun 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