bionic (1) scopparse.1e.gz

Provided by: embassy-domainatrix_0.1.660-2_amd64 bug

NAME
       scopparse - Generate DCF file from raw SCOP files.


SYNOPSIS
       scopparse -classfile infile -desinfile infile -nosegments boolean -nomultichain boolean
                 [-nominor boolean] -dcffile outfile

       scopparse -help


DESCRIPTION
       scopparse is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”).
       It is part of the "Utils:Database creation" command group(s).


OPTIONS
   Input section
       -classfile infile
           This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is
           the raw SCOP classification file available at
           http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57.

       -desinfile infile
           This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is
           the raw SCOP description file available at
           http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57.

   Required section
       -nosegments boolean
           This option specifies whether to omit domains comprising of more than one segment. This is necessary
           if a continuous residue sequence is required. Default value: N

       -nomultichain boolean
           This option specifies whether to omit domains comprising segments from more than one chain. This is
           necessary if a continuous residue sequence is required. Default value: N

   Additional section
       -nominor boolean
           This option specifies whether to omit domains from minor classes (defined as anything not in class
           'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta
           proteins (a+b)'). This is necessary or appropriate for many analyses. Default value: N

   Output section
       -dcffile outfile
           This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain
           classification file' contains classification and other data for domains from the SCOP or CATH
           databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence
           information can be added to the file by using DOMAINSEQS. Default value: test.scop


BUGS
       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to
       the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).


SEE ALSO
       scopparse is fully documented via the tfm(1) system.


AUTHOR
       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.


       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be
       redistributed under the same terms as EMBOSS itself.