Author: plessy Date: 2010-06-26 14:22:52 +0000 (Sat, 26 Jun 2010) New Revision: 4943
Modified: trunk/packages/embassy-domsearch/trunk/debian/changelog trunk/packages/embassy-domsearch/trunk/debian/control trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e Log: New upstream release (last January). Modified: trunk/packages/embassy-domsearch/trunk/debian/changelog =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/changelog 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/changelog 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,3 +1,15 @@ +embassy-domsearch (0.1.0++20100115-1) unstable; urgency=low + + * New upstream release in which the version number was unchanged. + (I chose a strange version number to avoid an epoch because of + the typo in the previous number). + * debian/control: + - Build against EMBOSS 6.2 (Closes: #587119). + - Checked conformance with Policy 3.8.4 (no changes needed). + * debian/*manpages* refreshed. + + -- Charles Plessy <[email protected]> Sat, 26 Jun 2010 22:58:36 +0900 + embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low * Initial release (Closes: #537204). Modified: trunk/packages/embassy-domsearch/trunk/debian/control =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/control 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/control 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,13 +1,13 @@ Source: embassy-domsearch Section: science Priority: optional -Build-Depends: cdbs, debhelper (>= 7), libajax6-dev, libnucleus6-dev, emboss-lib, libx11-dev, libgd2-xpm-dev +Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.2), libnucleus6-dev (>= 6.2), emboss-lib (>= 6.2), libx11-dev, libgd2-xpm-dev Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Charles Plessy <[email protected]> Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domsearch/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domsearch/trunk/ -Standards-Version: 3.8.2 +Standards-Version: 3.8.4 Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH Package: embassy-domsearch Modified: trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,5 +1,5 @@ +debian/manpages/seqsort.1e +debian/manpages/seqsearch.1e +debian/manpages/seqwords.1e debian/manpages/seqfraggle.1e debian/manpages/seqnr.1e -debian/manpages/seqsearch.1e -debian/manpages/seqsort.1e -debian/manpages/seqwords.1e Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,14 +1,23 @@ '\" t .\" Title: SEQFRAGGLE -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/16/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20980715 +.\" Source: EMBOSS 0.1.0++20100115 .\" Language: English .\" -.TH "SEQFRAGGLE" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian" +.TH "SEQFRAGGLE" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation @@ -34,7 +43,7 @@ .PP \fB\-dhfinpath\fR \fIdirlist\fR .RS 4 -This option specifies the location of DHF files (domain hits files) or other sequence files (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. 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\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./ +This option specifies the location of DHF files (domain hits files) or other sequence files (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. 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\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./ .RE .SS "Required section" .PP @@ -46,7 +55,7 @@ .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 -This option specifies the location of DHF files (domain hits files) (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. 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\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./ +This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. 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\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./ .RE .SH "BUGS" .PP @@ -58,7 +67,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,14 +1,23 @@ '\" t .\" Title: SEQNR -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/16/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20980715 +.\" Source: EMBOSS 0.1.0++20100115 .\" Language: English .\" -.TH "SEQNR" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian" +.TH "SEQNR" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation @@ -34,7 +43,7 @@ .PP \fB\-dhfinpath\fR \fIdirlist\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: \&./ +This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq 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 .PP \fB\-dosing\fR \fItoggle\fR @@ -44,7 +53,7 @@ .PP \fB\-singletsdir\fR \fIdirectory\fR .RS 4 -This option specifies the location of singlet filter sequences (e\&.g\&. DHF 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: \&./ +This option specifies the location of singlet filter sequences (e\&.g\&. DHF files) (input)\&. A \*(Aqdomain hits file\*(Aq 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 .PP \fB\-dosets\fR \fItoggle\fR @@ -54,7 +63,7 @@ .PP \fB\-insetsdir\fR \fIdirectory\fR .RS 4 -This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. 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: \&./ +This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. A \*(Aqdomain alignment file\*(Aq 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\-matrix\fR \fImatrixf\fR @@ -97,7 +106,7 @@ .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 -This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. 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: \&./ +This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq 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 .PP \fB\-dored\fR \fItoggle\fR @@ -107,7 +116,7 @@ .PP \fB\-redoutdir\fR \fIoutdir\fR .RS 4 -This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. 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: \&./ +This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq 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 .PP \fB\-logfile\fR \fIoutfile\fR @@ -124,7 +133,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,14 +1,23 @@ '\" t .\" Title: SEQSEARCH -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/16/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20980715 +.\" Source: EMBOSS 0.1.0++20100115 .\" Language: English .\" -.TH "SEQSEARCH" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian" +.TH "SEQSEARCH" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation @@ -39,7 +48,7 @@ .PP \fB\-inseqspath\fR \fIdirlist\fR .RS 4 -This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH 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: \&./ +This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH 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 \*(Aqdomain alignment file\*(Aq 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\-database\fR \fIstring\fR @@ -66,7 +75,7 @@ .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 -This option specifies the location of DHF files (domain hits files) (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA format\&. 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: \&./ +This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA format\&. 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 .PP \fB\-logfile\fR \fIoutfile\fR @@ -83,7 +92,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,14 +1,23 @@ '\" t .\" Title: SEQSORT -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/16/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20980715 +.\" Source: EMBOSS 0.1.0++20100115 .\" Language: English .\" -.TH "SEQSORT" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian" +.TH "SEQSORT" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation @@ -34,7 +43,7 @@ .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: \&./ +This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq 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 @@ -56,17 +65,17 @@ .PP \fB\-dhfoutdir\fR \fIoutdir\fR .RS 4 -This option specifies the location of DHF files (domain hits files) (output)\&. 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: \&./ +This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq 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 .PP \fB\-hitsfile\fR \fIoutfile\fR .RS 4 -This option specifies the name of domain families file (output)\&. A \'domain families file\' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \'domain ambiguities file\'\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf +This option specifies the name of domain families file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf .RE .PP \fB\-ambigfile\fR \fIoutfile\fR .RS 4 -This option specifies the name of domain ambiguities file (output)\&. A \'domain families file\' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \'domain ambiguities file\'\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf +This option specifies the name of domain ambiguities file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf .RE .SH "BUGS" .PP @@ -78,7 +87,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e =================================================================== --- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e 2010-06-26 09:56:01 UTC (rev 4942) +++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e 2010-06-26 14:22:52 UTC (rev 4943) @@ -1,14 +1,23 @@ '\" t .\" Title: SEQWORDS -.\" Author: Debian-Med Packaging Team <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/> -.\" Date: 07/16/2009 +.\" Author: Debian Med Packaging Team <[email protected]> +.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/> +.\" Date: 06/26/2010 .\" Manual: EMBOSS Manual for Debian -.\" Source: EMBOSS 0.1.0+20980715 +.\" Source: EMBOSS 0.1.0++20100115 .\" Language: English .\" -.TH "SEQWORDS" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian" +.TH "SEQWORDS" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation @@ -45,7 +54,7 @@ .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 -This option specifies the name of the DHF file (domain hits file) (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits +This option specifies the name of the DHF file (domain hits file) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits .RE .SH "BUGS" .PP @@ -57,7 +66,7 @@ system\&. .SH "AUTHOR" .PP -\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> +\fBDebian Med Packaging Team\fR <\&debian\-med\-packag...@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
