
                               scorecmapdir 



Function

   Contact scores for cleaned protein chain contact files

Description

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

Algorithm

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

Usage

   Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-cmapdir]           dirlist    Directory of cleaned-chain contact map files
  [-scoredcmapdir]     outdir     Directory where scored contact map files
                                  will be written
  [-outfileextension]  string     Appended to end of all output file names

   Additional (Optional) qualifiers:
   -contactscoringfile matrixf    Matrix of scores for frequency of contacts
                                  between specific amino acid residue types

   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
   [-cmapdir]
   (Parameter 1) Directory of cleaned-chain contact map files Directory
   with files ./contacttest/cmap
   [-scoredcmapdir]
   (Parameter 2) Directory where scored contact map files will be written
   Output directory ./contacttest/scored_cmap
   [-outfileextension]
   (Parameter 3) Appended to end of all output file names Any string is
   accepted .cmap2
   Additional (Optional) qualifiers Allowed values Default
   -contactscoringfile Matrix of scores for frequency of contacts between
   specific amino acid residue types Comparison matrix file in EMBOSS
   data path ./contacttest/testLOscores26Apr05.dat
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   scorecmapdir reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   scorecmapdir 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
   contactcount Count specific versus non-specific contacts
   contacts     Generate intra-chain CON files from CCF files
   domainalign  Generate alignments (DAF file) for nodes in a DCF file
   domainrep    Reorder DCF file to identify representative structures
   domainreso   Remove low resolution domains from a DCF file
   interface    Generate inter-chain CON files from CCF files
   libgen       Generate discriminating elements from alignments
   matgen3d     Generate a 3D-1D scoring matrix from CCF files
   psiphi       Phi and psi torsion angles from protein coordinates
   rocon        Generates a hits file from comparing two DHF files
   rocplot      Performs ROC analysis on hits files
   seqalign     Extend alignments (DAF file) with sequences (DHF file)
   seqfraggle   Removes fragment sequences from DHF files
   seqsearch    Generate PSI-BLAST hits (DHF file) from a DAF file
   seqsort      Remove ambiguous classified sequences from DHF files
   seqwords     Generates DHF files from keyword search of UniProt
   siggen       Generates a sparse protein signature from an alignment
   siggenlig    Generate ligand-binding signatures from a CON file
   sigscan      Generate hits (DHF file) from a signature search
   sigscanlig   Search ligand-signature library & write hits (LHF file)

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
