Author: plessy Date: 2009-07-17 04:43:46 +0000 (Fri, 17 Jul 2009) New Revision: 3649
Added: trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e Removed: trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1 trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1 trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1 trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1 Log: Moved the manpages from section 1 to 1e. Deleted: trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1 =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1 2009-07-16 14:00:54 UTC (rev 3648) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1 2009-07-17 04:43:46 UTC (rev 3649) @@ -1,78 +0,0 @@ -.\" Title: ALLVERSUSALL -.\" Author: Debian EMBOSS Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> -.\" Date: 09/26/2007 -.\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0 -.\" -.TH "ALLVERSUSALL" "1" "09/26/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "NAME" -allversusall - Sequence similarity data from all-versus-all comparison. -.SH "SYNOPSIS" -.HP 13 -\fBallversusall\fR \fB\-seqinpath\ \fR\fB\fIdirlist\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-datoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR -.HP 13 -\fBallversusall\fR \fB\-help\fR -.SH "DESCRIPTION" -.PP -\fBallversusall\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\-seqinpath\fR \fIdirlist\fR -.RS 4 -Default value: \./ -.RE -.PP -\fB\-matrix\fR \fImatrixf\fR -.RS 4 -This option specifies the residue substitution matrix that is used for sequence comparison\. Default value: EBLOSUM62 -.RE -.SS "Required section" -.SS "Additional section" -.PP -\fB\-gapopen\fR \fIfloat\fR -.RS 4 -This option specifies the gap insertion penalty\. The gap insertion penalty is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10 -.RE -.PP -\fB\-gapextend\fR \fIfloat\fR -.RS 4 -This option specifies the gap extension penalty\. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\. Default value: 0\.5 -.RE -.SS "Output section" -.PP -\fB\-datoutdir\fR \fIoutdir\fR -.RS 4 -This option specifies the location of sequence similarity data files (output)\. Default value: \./ -.RE -.PP -\fB\-logfile\fR \fIoutfile\fR -.RS 4 -This option specifies the name of ALLVERSUSALL log file (output)\. The log file contains messages about any errors arising while ALLVERSUSALL ran\. Default value: allversusall\.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 -allversusall is fully documented via the -\fBtfm\fR(1) -system\. -.SH "AUTHOR" -.PP -\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-de...@lists\.alioth\.debian\.org\&> -.sp -1n -.IP "" 4 -Wrote the script used to autogenerate this manual page\. -.SH "COPYRIGHT" -Copyright \(co 2007 Debian EMBOSS Packaging Team -.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 Copied: trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e (from rev 3648, trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1) =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e (rev 0) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e 2009-07-17 04:43:46 UTC (rev 3649) @@ -0,0 +1,87 @@ +'\" t +.\" Title: ALLVERSUSALL +.\" Author: Debian-Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> +.\" Date: 07/17/2009 +.\" Manual: EMBOSS Manual for Debian +.\" Source: EMBOSS 0.1.0+20090715 +.\" Language: English +.\" +.TH "ALLVERSUSALL" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +allversusall \- Sequence similarity data from all\-versus\-all comparison\&. +.SH "SYNOPSIS" +.HP \w'\fBallversusall\fR\ 'u +\fBallversusall\fR \fB\-seqinpath\ \fR\fB\fIdirlist\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-datoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR +.HP \w'\fBallversusall\fR\ 'u +\fBallversusall\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBallversusall\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\-seqinpath\fR \fIdirlist\fR +.RS 4 +Default value: \&./ +.RE +.PP +\fB\-matrix\fR \fImatrixf\fR +.RS 4 +This option specifies the residue substitution matrix that is used for sequence comparison\&. Default value: EBLOSUM62 +.RE +.SS "Required section" +.SS "Additional section" +.PP +\fB\-gapopen\fR \fIfloat\fR +.RS 4 +This option specifies the gap insertion penalty\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10 +.RE +.PP +\fB\-gapextend\fR \fIfloat\fR +.RS 4 +This option specifies the gap extension penalty\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: 0\&.5 +.RE +.SS "Output section" +.PP +\fB\-datoutdir\fR \fIoutdir\fR +.RS 4 +This option specifies the location of sequence similarity data files (output)\&. Default value: \&./ +.RE +.PP +\fB\-logfile\fR \fIoutfile\fR +.RS 4 +This option specifies the name of ALLVERSUSALL log file (output)\&. The log file contains messages about any errors arising while ALLVERSUSALL ran\&. Default value: allversusall\&.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 +allversusall is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +CopyrightCopyright \(co 2007 Debian-Med Packaging Team +.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 Property changes on: trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e ___________________________________________________________________ Added: svn:mergeinfo + Deleted: trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1 =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1 2009-07-16 14:00:54 UTC (rev 3648) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1 2009-07-17 04:43:46 UTC (rev 3649) @@ -1,92 +0,0 @@ -.\" Title: DOMAINALIGN -.\" Author: Debian EMBOSS Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> -.\" Date: 09/26/2007 -.\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0 -.\" -.TH "DOMAINALIGN" "1" "09/26/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "NAME" -domainalign - Generate alignments (DAF file) for nodes in a DCF file. -.SH "SYNOPSIS" -.HP 12 -\fBdomainalign\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-pdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-keepsinglets\ \fR\fB\fItoggle\fR\fR \fB\-dafoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-singletsoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-superoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR -.HP 12 -\fBdomainalign\fR \fB\-help\fR -.SH "DESCRIPTION" -.PP -\fBdomainalign\fR -is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Protein:3D Structure" command group(s)\. -.SH "OPTIONS" -.SS "Input section" -.PP -\fB\-dcfinfile\fR \fIinfile\fR -.RS 4 -This option specifies the name of DCF file (domain classification file) (input)\. 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\. -.RE -.PP -\fB\-pdbdir\fR \fIdirectory\fR -.RS 4 -This option specifies the location of domain PDB files (input)\. A \'domain PDB file\' contains coordinate data for a single domain from SCOP or CATH, in PDB format\. The files are generated by using DOMAINER\. Default value: \./ -.RE -.SS "Required section" -.PP -\fB\-node\fR \fIlist\fR -.RS 4 -This option specifies the node for redundancy removal\. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\. For example by selecting \'Class\' entries belonging to the same Class will be non\-redundant\. Default value: 1 -.RE -.PP -\fB\-mode\fR \fIlist\fR -.RS 4 -This option specifies the alignment algorithm to use\. Default value: 1 -.RE -.PP -\fB\-keepsinglets\fR \fItoggle\fR -.RS 4 -This option specifies whether to write sequences of singlet families to file\. If you specify this option, the sequence for each singlet family are written to file (output)\. Default value: Y -.RE -.SS "Output section" -.PP -\fB\-dafoutdir\fR \fIoutdir\fR -.RS 4 -This option specifies the location of DAF files (domain alignment files) (output)\. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\. The files are in clustal format and are annotated with domain family classification information\. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\. Default value: \./ -.RE -.PP -\fB\-singletsoutdir\fR \fIoutdir\fR -.RS 4 -This option specifies the location of DHF files (domain hits files) for singlet sequences (output)\. The singlets are written out as a \'domain hits file\' \- which contains database hits (sequences) with domain classification information, in FASTA format\. Default value: \./ -.RE -.PP -\fB\-superoutdir\fR \fIoutdir\fR -.RS 4 -This option specifies the location of structural superimposition files (output)\. A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used\. Default value: \./ -.RE -.PP -\fB\-logfile\fR \fIoutfile\fR -.RS 4 -This option specifies the name of log file (output)\. The log file contains messages about any errors arising while domainalign ran\. Default value: domainalign\.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 -domainalign is fully documented via the -\fBtfm\fR(1) -system\. -.SH "AUTHOR" -.PP -\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-de...@lists\.alioth\.debian\.org\&> -.sp -1n -.IP "" 4 -Wrote the script used to autogenerate this manual page\. -.SH "COPYRIGHT" -Copyright \(co 2007 Debian EMBOSS Packaging Team -.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 Copied: trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e (from rev 3648, trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1) =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e (rev 0) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e 2009-07-17 04:43:46 UTC (rev 3649) @@ -0,0 +1,101 @@ +'\" t +.\" Title: DOMAINALIGN +.\" Author: Debian-Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> +.\" Date: 07/17/2009 +.\" Manual: EMBOSS Manual for Debian +.\" Source: EMBOSS 0.1.0+20090715 +.\" Language: English +.\" +.TH "DOMAINALIGN" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +domainalign \- Generate alignments (DAF file) for nodes in a DCF file\&. +.SH "SYNOPSIS" +.HP \w'\fBdomainalign\fR\ 'u +\fBdomainalign\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-pdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-keepsinglets\ \fR\fB\fItoggle\fR\fR \fB\-dafoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-singletsoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-superoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR +.HP \w'\fBdomainalign\fR\ 'u +\fBdomainalign\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBdomainalign\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-dcfinfile\fR \fIinfile\fR +.RS 4 +This option specifies the name of DCF file (domain classification file) (input)\&. 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\&. +.RE +.PP +\fB\-pdbdir\fR \fIdirectory\fR +.RS 4 +This option specifies the location of domain PDB files (input)\&. A \'domain PDB file\' contains coordinate data for a single domain from SCOP or CATH, in PDB format\&. The files are generated by using DOMAINER\&. Default value: \&./ +.RE +.SS "Required section" +.PP +\fB\-node\fR \fIlist\fR +.RS 4 +This option specifies the node for redundancy removal\&. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\&. For example by selecting \'Class\' entries belonging to the same Class will be non\-redundant\&. Default value: 1 +.RE +.PP +\fB\-mode\fR \fIlist\fR +.RS 4 +This option specifies the alignment algorithm to use\&. Default value: 1 +.RE +.PP +\fB\-keepsinglets\fR \fItoggle\fR +.RS 4 +This option specifies whether to write sequences of singlet families to file\&. If you specify this option, the sequence for each singlet family are written to file (output)\&. Default value: Y +.RE +.SS "Output section" +.PP +\fB\-dafoutdir\fR \fIoutdir\fR +.RS 4 +This option specifies the location of DAF files (domain alignment files) (output)\&. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The files are in clustal format and are annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ +.RE +.PP +\fB\-singletsoutdir\fR \fIoutdir\fR +.RS 4 +This option specifies the location of DHF files (domain hits files) for singlet sequences (output)\&. The singlets are written out as a \'domain hits file\' \- which contains database hits (sequences) with domain classification information, in FASTA format\&. Default value: \&./ +.RE +.PP +\fB\-superoutdir\fR \fIoutdir\fR +.RS 4 +This option specifies the location of structural superimposition files (output)\&. A file in PDB format of the structural superimposition is generated for each family if the STAMP algorithm is used\&. Default value: \&./ +.RE +.PP +\fB\-logfile\fR \fIoutfile\fR +.RS 4 +This option specifies the name of log file (output)\&. The log file contains messages about any errors arising while domainalign ran\&. Default value: domainalign\&.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 +domainalign is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +CopyrightCopyright \(co 2007 Debian-Med Packaging Team +.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 Property changes on: trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e ___________________________________________________________________ Added: svn:mergeinfo + Deleted: trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1 =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1 2009-07-16 14:00:54 UTC (rev 3648) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1 2009-07-17 04:43:46 UTC (rev 3649) @@ -1,62 +0,0 @@ -.\" Title: DOMAINREP -.\" Author: Debian EMBOSS Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> -.\" Date: 09/26/2007 -.\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0 -.\" -.TH "DOMAINREP" "1" "09/26/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "NAME" -domainrep - Reorder DCF file to identify representative structures. -.SH "SYNOPSIS" -.HP 10 -\fBdomainrep\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR -.HP 10 -\fBdomainrep\fR \fB\-help\fR -.SH "DESCRIPTION" -.PP -\fBdomainrep\fR -is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Protein:3D Structure" command group(s)\. -.SH "OPTIONS" -.SS "Input section" -.PP -\fB\-dcfinfile\fR \fIinfile\fR -.RS 4 -This option specifies the name of DCF file (domain classification file) (input)\. 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\. -.RE -.SS "Required section" -.PP -\fB\-node\fR \fIlist\fR -.RS 4 -This option specifies the node fore reordering the file\. Reordering can be done for any specified node in the SCOP or CATH hierarchies\. For example by selecting \'Class\' entries belonging to the same Class will be reordered in turn\. Default value: 1 -.RE -.SS "Output section" -.PP -\fB\-dcfoutfile\fR \fIoutfile\fR -.RS 4 -This option specifies the name of 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: test\.scop -.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 -domainrep is fully documented via the -\fBtfm\fR(1) -system\. -.SH "AUTHOR" -.PP -\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-de...@lists\.alioth\.debian\.org\&> -.sp -1n -.IP "" 4 -Wrote the script used to autogenerate this manual page\. -.SH "COPYRIGHT" -Copyright \(co 2007 Debian EMBOSS Packaging Team -.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 Copied: trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e (from rev 3648, trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1) =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e (rev 0) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e 2009-07-17 04:43:46 UTC (rev 3649) @@ -0,0 +1,71 @@ +'\" t +.\" Title: DOMAINREP +.\" Author: Debian-Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> +.\" Date: 07/17/2009 +.\" Manual: EMBOSS Manual for Debian +.\" Source: EMBOSS 0.1.0+20090715 +.\" Language: English +.\" +.TH "DOMAINREP" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +domainrep \- Reorder DCF file to identify representative structures\&. +.SH "SYNOPSIS" +.HP \w'\fBdomainrep\fR\ 'u +\fBdomainrep\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR +.HP \w'\fBdomainrep\fR\ 'u +\fBdomainrep\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBdomainrep\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-dcfinfile\fR \fIinfile\fR +.RS 4 +This option specifies the name of DCF file (domain classification file) (input)\&. 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\&. +.RE +.SS "Required section" +.PP +\fB\-node\fR \fIlist\fR +.RS 4 +This option specifies the node fore reordering the file\&. Reordering can be done for any specified node in the SCOP or CATH hierarchies\&. For example by selecting \'Class\' entries belonging to the same Class will be reordered in turn\&. Default value: 1 +.RE +.SS "Output section" +.PP +\fB\-dcfoutfile\fR \fIoutfile\fR +.RS 4 +This option specifies the name of 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: test\&.scop +.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 +domainrep is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +CopyrightCopyright \(co 2007 Debian-Med Packaging Team +.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 Property changes on: trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e ___________________________________________________________________ Added: svn:mergeinfo + Deleted: trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1 =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1 2009-07-16 14:00:54 UTC (rev 3648) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1 2009-07-17 04:43:46 UTC (rev 3649) @@ -1,88 +0,0 @@ -.\" Title: SEQALIGN -.\" Author: Debian EMBOSS Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> -.\" Date: 09/26/2007 -.\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0 -.\" -.TH "SEQALIGN" "1" "09/26/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "NAME" -seqalign - Extend alignments (DAF file) with sequences (DHF file). -.SH "SYNOPSIS" -.HP 9 -\fBseqalign\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dafinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-amode\ \fR\fB\fIlist\fR\fR [\fB\-forcetype\ \fR\fB\fIboolean\fR\fR] \fB\-dafoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR -.HP 9 -\fBseqalign\fR \fB\-help\fR -.SH "DESCRIPTION" -.PP -\fBseqalign\fR -is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Protein:3D Structure" command group(s)\. -.SH "OPTIONS" -.SS "Input section" -.PP -\fB\-mode\fR \fIlist\fR -.RS 4 -This option specifies the mode of SEQALIGN operation\. SEQALIGN takes as input a directory of either i\. single sequences, ii\. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file))\. The user has to specify which\. Default value: 1 -.RE -.PP -\fB\-dhfinpath\fR \fIdirlist\fR -.RS 4 -This option specifies the location of sequences, e\.g\. DHF files (domain hits files) (input)\. SEQALIGN takes as input a database of either i\. single sequences, ii\. sets of unaligned sequences or iii\. sets of aligned sequences, e\.g\. a domain alignment file\. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\. The file is in clustal format annotated with domain family classification information\. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\. Default value: \./ -.RE -.PP -\fB\-dafinpath\fR \fIdirlist\fR -.RS 4 -This option specifies the location of sequences, e\.g\. DAF files (domain alignment files) (input)\. SEQALIGN takes as input a database of either i\. single sequences, ii\. sets of unaligned sequences or iii\. sets of aligned sequences, e\.g\. a domain alignment file\. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\. The file is in clustal format annotated with domain family classification information\. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\. Default value: \./ -.RE -.PP -\fB\-dhfindir\fR \fIdirectory\fR -.RS 4 -This option specifies the location of DHF files (domain hits files) (input)\. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\. Default value: \./ -.RE -.SS "Required section" -.PP -\fB\-amode\fR \fIlist\fR -.RS 4 -This option specifies which alignment algorithm to use\. Default value: 1 -.RE -.SS "Additional section" -.PP -\fB\-forcetype\fR \fIboolean\fR -.RS 4 -This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available Default value: N -.RE -.SS "Output section" -.PP -\fB\-dafoutdir\fR \fIoutdir\fR -.RS 4 -This option specifies the location of DAF files (domain alignment files) (output)\. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\. The file is in clustal format annotated with domain family classification information\. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\. Default value: \./ -.RE -.PP -\fB\-logfile\fR \fIoutfile\fR -.RS 4 -This option specifies the name of log file for the build\. The log file contains messages about any errors arising while SEQALIGN ran\. Default value: seqalign\.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 -seqalign is fully documented via the -\fBtfm\fR(1) -system\. -.SH "AUTHOR" -.PP -\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-de...@lists\.alioth\.debian\.org\&> -.sp -1n -.IP "" 4 -Wrote the script used to autogenerate this manual page\. -.SH "COPYRIGHT" -Copyright \(co 2007 Debian EMBOSS Packaging Team -.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 Copied: trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e (from rev 3648, trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1) =================================================================== --- trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e (rev 0) +++ trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e 2009-07-17 04:43:46 UTC (rev 3649) @@ -0,0 +1,97 @@ +'\" t +.\" Title: SEQALIGN +.\" Author: Debian-Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> +.\" Date: 07/17/2009 +.\" Manual: EMBOSS Manual for Debian +.\" Source: EMBOSS 0.1.0+20090715 +.\" Language: English +.\" +.TH "SEQALIGN" "1e" "07/17/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian" +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +seqalign \- Extend alignments (DAF file) with sequences (DHF file)\&. +.SH "SYNOPSIS" +.HP \w'\fBseqalign\fR\ 'u +\fBseqalign\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dafinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-amode\ \fR\fB\fIlist\fR\fR [\fB\-forcetype\ \fR\fB\fIboolean\fR\fR] \fB\-dafoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR +.HP \w'\fBseqalign\fR\ 'u +\fBseqalign\fR \fB\-help\fR +.SH "DESCRIPTION" +.PP +\fBseqalign\fR +is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&. +.SH "OPTIONS" +.SS "Input section" +.PP +\fB\-mode\fR \fIlist\fR +.RS 4 +This option specifies the mode of SEQALIGN operation\&. SEQALIGN takes as input a directory of either i\&. single sequences, ii\&. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file))\&. The user has to specify which\&. Default value: 1 +.RE +.PP +\fB\-dhfinpath\fR \fIdirlist\fR +.RS 4 +This option specifies the location of sequences, e\&.g\&. DHF files (domain hits files) (input)\&. SEQALIGN takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ +.RE +.PP +\fB\-dafinpath\fR \fIdirlist\fR +.RS 4 +This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQALIGN takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ +.RE +.PP +\fB\-dhfindir\fR \fIdirectory\fR +.RS 4 +This option specifies the location of DHF files (domain hits files) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&. Default value: \&./ +.RE +.SS "Required section" +.PP +\fB\-amode\fR \fIlist\fR +.RS 4 +This option specifies which alignment algorithm to use\&. Default value: 1 +.RE +.SS "Additional section" +.PP +\fB\-forcetype\fR \fIboolean\fR +.RS 4 +This option specifies whether to force minimal domain classification data to be written to the output file in cases where singlet sequences were given as input file and no classification data was available Default value: N +.RE +.SS "Output section" +.PP +\fB\-dafoutdir\fR \fIoutdir\fR +.RS 4 +This option specifies the location of DAF files (domain alignment files) (output)\&. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./ +.RE +.PP +\fB\-logfile\fR \fIoutfile\fR +.RS 4 +This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while SEQALIGN ran\&. Default value: seqalign\&.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 +seqalign is fully documented via the +\fBtfm\fR(1) +system\&. +.SH "AUTHOR" +.PP +\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +.RS 4 +Wrote the script used to autogenerate this manual page\&. +.RE +.SH "COPYRIGHT" +.br +CopyrightCopyright \(co 2007 Debian-Med Packaging Team +.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 Property changes on: trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e ___________________________________________________________________ Added: svn:mergeinfo + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
