EMBOSS: scopparse

Program scopparse

Function

Reads raw-, and writes EMBL-like, scop classification files

Description

This is part of Jon Ison's protein structure analysis package.

This package is still being developed.

Please ignore this program until further details can be documented.

All further queries should go to Jon Ison. (Jon Ison)

Usage

Here is a sample session with scopparse: 

% scopparse

Command line arguments 

   Mandatory qualifiers:
  [-infilea]           infile     Name of scop classification file for input
                                  (raw format dir.cla.scop.txt_X.XX file)
  [-infileb]           infile     Name of description file for input (raw
                                  format dir.des.scop.txt_X.XX file)
  [-outfile]           outfile    Name of scop file for output (embl-like
                                  format)

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose

Mandatory qualifiers Allowed values Default
[-infilea]
(Parameter 1)		 Name of scop classification file for input (raw format dir.cla.scop.txt_X.XX file) Input file dir.cla.scop.txt_1.57
[-infileb]
(Parameter 2)		 Name of description file for input (raw format dir.des.scop.txt_X.XX file) Input file dir.des.scop.txt_1.57
[-outfile]
(Parameter 3)		 Name of scop file for output (embl-like format) Output file Escop.dat
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Output file format

Data files

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
cutgextractExtract data from CUTG
domainerBuild domain coordinate files
nrscopeConverts redundant EMBL-format SCOP file to non-redundant one
pdbtospConvert raw swissprot:pdb equivalence file to embl-like format
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE
scopeConvert raw scop classification file to embl-like format
seqnrConverts redundant database results to a non-redundant set of hits
tfextractExtract data from TRANSFAC

Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

History

Written (date) - author.

Target users

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

Comments