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scopparse(1e) [debian man page]

SCOPPARSE(1e)						     EMBOSS Manual for Debian						     SCOPPARSE(1e)

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.

COPYRIGHT

       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.

DOMAINATRIX 0.1.0+20100721					    08/11/2010							     SCOPPARSE(1e)

Check Out this Related Man Page

CATHPARSE(1e)						     EMBOSS Manual for Debian						     CATHPARSE(1e)

NAME

       cathparse - Generates DCF file from raw CATH files.

SYNOPSIS

       cathparse -listfile infile -domfile infile -namesfile infile -outfile outfile -logfile outfile

       cathparse -help

DESCRIPTION

       cathparse 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
       -listfile infile
	   This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification
	   and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). Default value: caths.list.v2.4

       -domfile infile
	   This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and
	   description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). Default value: domlist.v2.4

       -namesfile infile
	   This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files
	   (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). Default value: CAT.names.all.v2.4

   Output section
       -outfile outfile
	   This option specifies the name of CATH DCF file (domain classification file) (output). A 'domain classification file' contains
	   classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and
	   CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. Default value: Ecath.dat

       -logfile outfile
	   This option specifies the name of the CATHPARSE log file. Default value: cathparse.log

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

       cathparse 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.

COPYRIGHT

       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.

DOMAINATRIX 0.1.0+20100721					    08/11/2010							     CATHPARSE(1e)
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