[med-svn] r13066 - in trunk/packages/aragorn/trunk/debian: . man patches
Sascha Steinbiss
sascha-guest at alioth.debian.org
Sat Feb 23 09:50:39 UTC 2013
Author: sascha-guest
Date: 2013-02-23 09:50:39 +0000 (Sat, 23 Feb 2013)
New Revision: 13066
Modified:
trunk/packages/aragorn/trunk/debian/changelog
trunk/packages/aragorn/trunk/debian/man/aragorn.1
trunk/packages/aragorn/trunk/debian/manpage.1.src
trunk/packages/aragorn/trunk/debian/patches/series
trunk/packages/aragorn/trunk/debian/watch
Log:
adjust for 1.2.36, waiting for upstream to publish source
Modified: trunk/packages/aragorn/trunk/debian/changelog
===================================================================
--- trunk/packages/aragorn/trunk/debian/changelog 2013-02-23 09:50:24 UTC (rev 13065)
+++ trunk/packages/aragorn/trunk/debian/changelog 2013-02-23 09:50:39 UTC (rev 13066)
@@ -1,5 +1,5 @@
-aragorn (1.2.34-1) unstable; urgency=low
+aragorn (1.2.36-1) unstable; urgency=low
* Initial release (Closes: #nnnn)
- -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Wed, 06 Feb 2013 10:02:30 +0100
+ -- Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de> Wed, 16 Feb 2013 10:02:30 +0100
Modified: trunk/packages/aragorn/trunk/debian/man/aragorn.1
===================================================================
--- trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-02-23 09:50:24 UTC (rev 13065)
+++ trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-02-23 09:50:39 UTC (rev 13066)
@@ -2,12 +2,12 @@
.\" Title: aragorn
.\" Author: [see the "AUTHORS" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 02/09/2013
+.\" Date: 02/23/2013
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "ARAGORN" "1" "02/09/2013" "\ \&" "\ \&"
+.TH "ARAGORN" "1" "02/23/2013" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -117,7 +117,10 @@
strand of each sequence\&.
\-ps Lower scoring thresholds to 95% of default levels\&.
\-ps<num> Change scoring thresholds to <num> percent of default levels\&.
-\-rp Report possible pseudogenes (normalised score < 100)\&.
+\-rp Flag possible pseudogenes (score < 100 or tRNA anticodon
+ loop <> 7 bases long)\&. Note that genes with score < 100
+ will not be detected or flagged if scoring thresholds are not
+ also changed to below 100% (see \-ps switch)\&.
\-seq Print out primary sequence\&.
\-br Show secondary structure of tRNA gene primary sequence
using round brackets\&.
@@ -161,9 +164,9 @@
<filename> is assumed to contain one or more sequences in FASTA format\&. Results of the search are printed to STDOUT\&. All switches are optional and case\-insensitive\&. Unless \-i is specified, tRNA genes containing introns are not detected\&.
.SH "AUTHORS"
.sp
-Bjorn Canback <bcanback at acgt\&.se>, Dean Laslett <gaiaquark at gmail\&.com >
+Bjorn Canback <bcanback at acgt\&.se>, Dean Laslett <gaiaquark at gmail\&.com>
.SH "REFERENCES"
.sp
Laslett, D\&. and Canback, B\&. (2004) ARAGORN, a program for the detection of transfer RNA and transfer\-messenger RNA genes in nucleotide sequences Nucleic Acids Research, 32;11\-16
.sp
-Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&.
+Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&.
Modified: trunk/packages/aragorn/trunk/debian/manpage.1.src
===================================================================
--- trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-02-23 09:50:24 UTC (rev 13065)
+++ trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-02-23 09:50:39 UTC (rev 13066)
@@ -1,166 +1,169 @@
-ARAGORN(1)
-==========
-
-NAME
-----
-
-aragorn - detect tRNA genes in nucleotide sequences
-
-
-SYNOPSIS
---------
-
-*aragorn* -v -s -d -c -l -j -a -q -rn -w -ifro<min>,<max> -t -m -mt
- -gc -tv -seq -br -fasta -fo -o <outfile> <filename>
-
-
-OPTIONS
--------
-
- -m Search for tmRNA genes.
- -t Search for tRNA genes.
- By default, all are detected. If one of
- -m or -t is specified, then the other
- is not detected unless specified as well.
- -mt Search for Metazoan mitochondrial tRNA genes.
- tRNA genes with introns not detected. -i,-sr switchs
- ignored. Composite Metazoan mitochondrial
- genetic code used.
- -mtmam Search for Mammalian mitochondrial tRNA
- genes. -i,-sr switchs ignored. -tv switch set.
- Mammalian mitochondrial genetic code used.
- -mtx Same as -mt but low scoring tRNA genes are
- not reported.
- -mtd Overlapping metazoan mitochondrial tRNA genes
- on opposite strands are reported.
- -gc<num> Use the GenBank transl_table = <num> genetic code.
- -gcstd Use standard genetic code.
- -gcmet Use composite Metazoan mitochondrial genetic code.
- -gcvert Use Vertebrate mitochondrial genetic code.
- -gcinvert Use Invertebrate mitochondrial genetic code.
- -gcyeast Use Yeast mitochondrial genetic code.
- -gcprot Use Mold/Protozoan/Coelenterate mitochondrial genetic code.
- -gcciliate Use Ciliate genetic code.
- -gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code
- -gceuplot Use Euplotid genetic code.
- -gcbact Use Bacterial/Plant Chloroplast genetic code.
- -gcaltyeast Use alternative Yeast genetic code.
- -gcascid Use Ascidian Mitochondrial genetic code.
- -gcaltflat Use alternative Flatworm Mitochondrial genetic code.
- -gcblep Use Blepharisma genetic code.
- -gcchloroph Use Chlorophycean Mitochondrial genetic code.
- -gctrem Use Trematode Mitochondrial genetic code.
- -gcscen Use Scenedesmus obliquus Mitochondrial genetic code.
- -gcthraust Use Thraustochytrium Mitochondrial genetic code.
- Individual modifications can be appended using
- ,BBB=<aa> B = A,C,G, or T. <aa> is the three letter
- code for an amino-acid. More than one modification
- can be specified. eg -gcvert,aga=Trp,agg=Trp uses
- the Vertebrate Mitochondrial code and the codons
- AGA and AGG changed to Tryptophan.
- -tv Do not search for mitochondrial TV replacement
- loop tRNA genes. Only relevant if -mt used.
- -c7 Search for tRNA genes with 7 base C-loops only.
- -i Search for tRNA genes with introns in
- anticodon loop with maximum length 3000
- bases. Minimum intron length is 0 bases.
- Ignored if -m is specified.
- -i<max> Search for tRNA genes with introns in
- anticodon loop with maximum length <max>
- bases. Minimum intron length is 0 bases.
- Ignored if -m is specified.
- -i<min>,<max> Search for tRNA genes with introns in
- anticodon loop with maximum length <max>
- bases, and minimum length <min> bases.
- Ignored if -m is specified.
- -io Same as -i, but allow tRNA genes with long
- introns to overlap shorter tRNA genes.
- -if Same as -i, but fix intron between positions
- 37 and 38 on C-loop (one base after anticodon).
- -ifo Same as -if and -io combined.
- -ir Same as -i, but report tRNA genes with minimum
- length <min> bases rather than search for
- tRNA genes with minimum length <min> bases.
- With this switch, <min> acts as an output filter,
- minimum intron length for searching is still 0 bases.
- -c Assume that each sequence has a circular
- topology. Search wraps around each end.
- Default setting.
- -l Assume that each sequence has a linear
- topology. Search does not wrap.
- -d Double. Search both strands of each
- sequence. Default setting.
- -s or -s+ Single. Do not search the complementary
- (antisense) strand of each sequence.
- -sc or -s- Single complementary. Do not search the sense
- strand of each sequence.
- -ps Lower scoring thresholds to 95% of default levels.
- -ps<num> Change scoring thresholds to <num> percent of default levels.
- -rp Report possible pseudogenes (normalised score < 100).
- -seq Print out primary sequence.
- -br Show secondary structure of tRNA gene primary sequence
- using round brackets.
- -fasta Print out primary sequence in fasta format.
- -fo Print out primary sequence in fasta format only
- (no secondary structure).
- -fon Same as -fo, with sequence and gene numbering in header.
- -fos Same as -fo, with no spaces in header.
- -fons Same as -fo, with sequence and gene numbering, but no spaces.
- -w Print out in Batch mode.
- -ss Use the stricter canonical 1-2 bp spacer1 and
- 1 bp spacer2. Ignored if -mt set. Default is to
- allow 3 bp spacer1 and 0-2 bp spacer2, which may
- degrade selectivity.\n");
- -v Verbose. Prints out information during
- search to STDERR.
- -a Print out tRNA domain for tmRNA genes.
- -a7 Restrict tRNA astem length to a maximum of 7 bases
- -aa Display message if predicted iso-acceptor species
- does not match species in sequence name (if present).
- -j Display 4-base sequence on 3' end of astem
- regardless of predicted amino-acyl acceptor length.
- -jr Allow some divergence of 3' amino-acyl acceptor
- sequence from NCCA.
- -jr4 Allow some divergence of 3' amino-acyl acceptor
- sequence from NCCA, and display 4 bases.
- -q Dont print configuration line (which switchs
- and files were used).
- -rn Repeat sequence name before summary information.
- -O <outfile> Print output to <outfile>. If <outfile>
- already exists, it is overwritten. By default
- all output goes to stdout.
-
-DESCRIPTION
------------
-
-aragorn detects tRNA, mtRNA, and tmRNA genes.
-A minimum requirement is at least a 32 bit compiler architecture
-(variable types int and unsigned int are at least 4 bytes long).
-
-<filename> is assumed to contain one or more sequences
-in FASTA format. Results of the search are printed to
-STDOUT. All switches are optional and case-insensitive.
-Unless -i is specified, tRNA genes containing introns
-are not detected.
-
-
-AUTHORS
-------
-
-Bjorn Canback <bcanback at acgt.se>, Dean Laslett <gaiaquark at gmail.com >
-
-
-REFERENCES
-----------
-
-Laslett, D. and Canback, B. (2004) ARAGORN, a
-program for the detection of transfer RNA and transfer-messenger
-RNA genes in nucleotide sequences
-Nucleic Acids Research, 32;11-16
-
-Laslett, D. and Canback, B. (2008) ARWEN: a
-program to in metazoan mitochondrial
-nucleotide sequences
-Bioinformatics, 24(2); 172-175.
-
-
+ARAGORN(1)
+==========
+
+NAME
+----
+
+aragorn - detect tRNA genes in nucleotide sequences
+
+
+SYNOPSIS
+--------
+
+*aragorn* -v -s -d -c -l -j -a -q -rn -w -ifro<min>,<max> -t -m -mt
+ -gc -tv -seq -br -fasta -fo -o <outfile> <filename>
+
+
+OPTIONS
+-------
+
+ -m Search for tmRNA genes.
+ -t Search for tRNA genes.
+ By default, all are detected. If one of
+ -m or -t is specified, then the other
+ is not detected unless specified as well.
+ -mt Search for Metazoan mitochondrial tRNA genes.
+ tRNA genes with introns not detected. -i,-sr switchs
+ ignored. Composite Metazoan mitochondrial
+ genetic code used.
+ -mtmam Search for Mammalian mitochondrial tRNA
+ genes. -i,-sr switchs ignored. -tv switch set.
+ Mammalian mitochondrial genetic code used.
+ -mtx Same as -mt but low scoring tRNA genes are
+ not reported.
+ -mtd Overlapping metazoan mitochondrial tRNA genes
+ on opposite strands are reported.
+ -gc<num> Use the GenBank transl_table = <num> genetic code.
+ -gcstd Use standard genetic code.
+ -gcmet Use composite Metazoan mitochondrial genetic code.
+ -gcvert Use Vertebrate mitochondrial genetic code.
+ -gcinvert Use Invertebrate mitochondrial genetic code.
+ -gcyeast Use Yeast mitochondrial genetic code.
+ -gcprot Use Mold/Protozoan/Coelenterate mitochondrial genetic code.
+ -gcciliate Use Ciliate genetic code.
+ -gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code
+ -gceuplot Use Euplotid genetic code.
+ -gcbact Use Bacterial/Plant Chloroplast genetic code.
+ -gcaltyeast Use alternative Yeast genetic code.
+ -gcascid Use Ascidian Mitochondrial genetic code.
+ -gcaltflat Use alternative Flatworm Mitochondrial genetic code.
+ -gcblep Use Blepharisma genetic code.
+ -gcchloroph Use Chlorophycean Mitochondrial genetic code.
+ -gctrem Use Trematode Mitochondrial genetic code.
+ -gcscen Use Scenedesmus obliquus Mitochondrial genetic code.
+ -gcthraust Use Thraustochytrium Mitochondrial genetic code.
+ Individual modifications can be appended using
+ ,BBB=<aa> B = A,C,G, or T. <aa> is the three letter
+ code for an amino-acid. More than one modification
+ can be specified. eg -gcvert,aga=Trp,agg=Trp uses
+ the Vertebrate Mitochondrial code and the codons
+ AGA and AGG changed to Tryptophan.
+ -tv Do not search for mitochondrial TV replacement
+ loop tRNA genes. Only relevant if -mt used.
+ -c7 Search for tRNA genes with 7 base C-loops only.
+ -i Search for tRNA genes with introns in
+ anticodon loop with maximum length 3000
+ bases. Minimum intron length is 0 bases.
+ Ignored if -m is specified.
+ -i<max> Search for tRNA genes with introns in
+ anticodon loop with maximum length <max>
+ bases. Minimum intron length is 0 bases.
+ Ignored if -m is specified.
+ -i<min>,<max> Search for tRNA genes with introns in
+ anticodon loop with maximum length <max>
+ bases, and minimum length <min> bases.
+ Ignored if -m is specified.
+ -io Same as -i, but allow tRNA genes with long
+ introns to overlap shorter tRNA genes.
+ -if Same as -i, but fix intron between positions
+ 37 and 38 on C-loop (one base after anticodon).
+ -ifo Same as -if and -io combined.
+ -ir Same as -i, but report tRNA genes with minimum
+ length <min> bases rather than search for
+ tRNA genes with minimum length <min> bases.
+ With this switch, <min> acts as an output filter,
+ minimum intron length for searching is still 0 bases.
+ -c Assume that each sequence has a circular
+ topology. Search wraps around each end.
+ Default setting.
+ -l Assume that each sequence has a linear
+ topology. Search does not wrap.
+ -d Double. Search both strands of each
+ sequence. Default setting.
+ -s or -s+ Single. Do not search the complementary
+ (antisense) strand of each sequence.
+ -sc or -s- Single complementary. Do not search the sense
+ strand of each sequence.
+ -ps Lower scoring thresholds to 95% of default levels.
+ -ps<num> Change scoring thresholds to <num> percent of default levels.
+ -rp Flag possible pseudogenes (score < 100 or tRNA anticodon
+ loop <> 7 bases long). Note that genes with score < 100
+ will not be detected or flagged if scoring thresholds are not
+ also changed to below 100% (see -ps switch).
+ -seq Print out primary sequence.
+ -br Show secondary structure of tRNA gene primary sequence
+ using round brackets.
+ -fasta Print out primary sequence in fasta format.
+ -fo Print out primary sequence in fasta format only
+ (no secondary structure).
+ -fon Same as -fo, with sequence and gene numbering in header.
+ -fos Same as -fo, with no spaces in header.
+ -fons Same as -fo, with sequence and gene numbering, but no spaces.
+ -w Print out in Batch mode.
+ -ss Use the stricter canonical 1-2 bp spacer1 and
+ 1 bp spacer2. Ignored if -mt set. Default is to
+ allow 3 bp spacer1 and 0-2 bp spacer2, which may
+ degrade selectivity.\n");
+ -v Verbose. Prints out information during
+ search to STDERR.
+ -a Print out tRNA domain for tmRNA genes.
+ -a7 Restrict tRNA astem length to a maximum of 7 bases
+ -aa Display message if predicted iso-acceptor species
+ does not match species in sequence name (if present).
+ -j Display 4-base sequence on 3' end of astem
+ regardless of predicted amino-acyl acceptor length.
+ -jr Allow some divergence of 3' amino-acyl acceptor
+ sequence from NCCA.
+ -jr4 Allow some divergence of 3' amino-acyl acceptor
+ sequence from NCCA, and display 4 bases.
+ -q Dont print configuration line (which switchs
+ and files were used).
+ -rn Repeat sequence name before summary information.
+ -O <outfile> Print output to <outfile>. If <outfile>
+ already exists, it is overwritten. By default
+ all output goes to stdout.
+
+DESCRIPTION
+-----------
+
+aragorn detects tRNA, mtRNA, and tmRNA genes.
+A minimum requirement is at least a 32 bit compiler architecture
+(variable types int and unsigned int are at least 4 bytes long).
+
+<filename> is assumed to contain one or more sequences
+in FASTA format. Results of the search are printed to
+STDOUT. All switches are optional and case-insensitive.
+Unless -i is specified, tRNA genes containing introns
+are not detected.
+
+
+AUTHORS
+------
+
+Bjorn Canback <bcanback at acgt.se>, Dean Laslett <gaiaquark at gmail.com>
+
+
+REFERENCES
+----------
+
+Laslett, D. and Canback, B. (2004) ARAGORN, a
+program for the detection of transfer RNA and transfer-messenger
+RNA genes in nucleotide sequences
+Nucleic Acids Research, 32;11-16
+
+Laslett, D. and Canback, B. (2008) ARWEN: a
+program to detect tRNA genes in metazoan mitochondrial
+nucleotide sequences
+Bioinformatics, 24(2); 172-175.
+
+
Modified: trunk/packages/aragorn/trunk/debian/patches/series
===================================================================
--- trunk/packages/aragorn/trunk/debian/patches/series 2013-02-23 09:50:24 UTC (rev 13065)
+++ trunk/packages/aragorn/trunk/debian/patches/series 2013-02-23 09:50:39 UTC (rev 13066)
@@ -1,2 +0,0 @@
-formatstrings
-hardening
Modified: trunk/packages/aragorn/trunk/debian/watch
===================================================================
--- trunk/packages/aragorn/trunk/debian/watch 2013-02-23 09:50:24 UTC (rev 13065)
+++ trunk/packages/aragorn/trunk/debian/watch 2013-02-23 09:50:39 UTC (rev 13066)
@@ -1,9 +1,2 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# See uscan(1) for format
-
-# Compulsory line, this is a version 3 file
version=3
-
http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn(.*).c
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