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'\" t
.\" Title: CATHPARSE
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\" Date: 08/11/2010
.\" Manual: EMBOSS Manual for Debian
.\" Source: DOMAINATRIX 0.1.0+20100721
.\" Language: English
.\"
.TH "CATHPARSE" "1e" "08/11/2010" "DOMAINATRIX 0.1.0+20100721" "EMBOSS Manual for Debian"
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.SH "NAME"
cathparse \- Generates DCF file from raw CATH files\&.
.SH "SYNOPSIS"
.HP \w'\fBcathparse\fR\ 'u
\fBcathparse\fR \fB\-listfile\ \fR\fB\fIinfile\fR\fR \fB\-domfile\ \fR\fB\fIinfile\fR\fR \fB\-namesfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBcathparse\fR\ 'u
\fBcathparse\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBcathparse\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-listfile\fR \fIinfile\fR
.RS 4
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
.RE
.PP
\fB\-domfile\fR \fIinfile\fR
.RS 4
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
.RE
.PP
\fB\-namesfile\fR \fIinfile\fR
.RS 4
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
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of CATH DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq 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
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
.RS 4
This option specifies the name of the CATHPARSE log file\&. Default value: cathparse\&.log
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
cathparse is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
.sp
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