[med-svn] r12374 - in trunk/packages/genometools/trunk/debian: . man
Sascha Steinbiss
sascha-guest at alioth.debian.org
Wed Oct 10 22:20:54 UTC 2012
Author: sascha-guest
Date: 2012-10-10 22:20:53 +0000 (Wed, 10 Oct 2012)
New Revision: 12374
Added:
trunk/packages/genometools/trunk/debian/man/gt-csa.1
Modified:
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1
trunk/packages/genometools/trunk/debian/man/gt-hop.1
trunk/packages/genometools/trunk/debian/rules
Log:
minor lintian cleanups
Modified: trunk/packages/genometools/trunk/debian/control
===================================================================
--- trunk/packages/genometools/trunk/debian/control 2012-10-10 19:34:52 UTC (rev 12373)
+++ trunk/packages/genometools/trunk/debian/control 2012-10-10 22:20:53 UTC (rev 12374)
@@ -54,8 +54,13 @@
libgenometools0 (= ${binary:Version})
Section: libdevel
Description: development files for GenomeTools
- This package contains the GenomeTools static libraries and necessary
+ This package contains the GenomeTools static library and necessary
header files.
+ .
+ Besides basic bioinformatics data structures, the library contains components
+ for sequence and annotation handling, sequence compression, index structure
+ generation and access, efficient matching, annotation visualization and much
+ more.
Package: genometools-doc
Architecture: all
@@ -63,7 +68,9 @@
Section: doc
Description: documentation for GenomeTools
This package contains API documentation and tool documentation for
- GenomeTools.
+ GenomeTools. The GenomeTools toolkit contains binaries for sequence and
+ annotation handling, sequence compression, index structure generation and
+ access, annotation visualization, and much more.
Package: genometools-dbg
Architecture: any
Added: trunk/packages/genometools/trunk/debian/man/gt-csa.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-csa.1 (rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-csa.1 2012-10-10 22:20:53 UTC (rev 12374)
@@ -0,0 +1,142 @@
+'\" t
+.\" Title: gt-csa
+.\" Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 10/10/2012
+.\" Manual: \ \&
+.\" Source: \ \&
+.\" Language: English
+.\"
+.TH "GT\-CSA" "1" "10/10/2012" "\ \&" "\ \&"
+.\" -----------------------------------------------------------------
+.\" * 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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+gt-csa \- Transform spliced alignments from GFF3 file into consensus spliced alignments\&.
+.SH "SYNOPSIS"
+.sp
+gt csa [option \&...] [GFF3_file]
+.SH "OPTIONS"
+.PP
+\fB\-join\-length\fR
+.RS 4
+set join length for the spliced alignment clustering (default: 300)
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+be verbose (default: no)
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+redirect output to specified file (default: undefined)
+.RE
+.PP
+\fB\-gzip\fR
+.RS 4
+write gzip compressed output file (default: no)
+.RE
+.PP
+\fB\-bzip2\fR
+.RS 4
+write bzip2 compressed output file (default: no)
+.RE
+.PP
+\fB\-force\fR
+.RS 4
+force writing to output file (default: no)
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+display help and exit
+.RE
+.PP
+\fB\-version\fR
+.RS 4
+display version information and exit
+.RE
+.SH "DESCRIPTION"
+.sp
+Let\(cqs assume we have a GFF3 file \fIcsa_example_spliced_alignments\&.gff3\fR containing the following four overlapping spliced alignments (represented as genes with exons as children):
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+##gff\-version 3
+##sequence\-region seq 1 290
+seq \&. gene 1 209 \&. + \&. ID=gene1
+seq \&. exon 1 90 \&. + \&. Parent=gene1
+seq \&. exon 110 190 \&. + \&. Parent=gene1
+seq \&. exon 201 209 \&. + \&. Parent=gene1
+###
+seq \&. gene 1 290 \&. + \&. ID=gene2
+seq \&. exon 1 90 \&. + \&. Parent=gene2
+seq \&. exon 101 190 \&. + \&. Parent=gene2
+seq \&. exon 201 290 \&. + \&. Parent=gene2
+###
+seq \&. gene 10 290 \&. + \&. ID=gene3
+seq \&. exon 10 90 \&. + \&. Parent=gene3
+seq \&. exon 110 190 \&. + \&. Parent=gene3
+seq \&. exon 201 290 \&. + \&. Parent=gene3
+###
+seq \&. gene 181 290 \&. + \&. ID=gene4
+seq \&. exon 181 190 \&. + \&. Parent=gene4
+seq \&. exon 201 290 \&. + \&. Parent=gene4
+###
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+To compute the consensus spliced alignments we call:
+.sp
+$ gt csa csa_example_spliced_alignments\&.gff3
+.sp
+Which returns:
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+##gff\-version 3
+##sequence\-region seq 1 290
+seq gt csa gene 1 290 \&. + \&. ID=gene1
+seq gt csa mRNA 1 290 \&. + \&. ID=mRNA1;Parent=gene1
+seq gt csa exon 1 90 \&. + \&. Parent=mRNA1
+seq gt csa exon 110 190 \&. + \&. Parent=mRNA1
+seq gt csa exon 201 290 \&. + \&. Parent=mRNA1
+seq gt csa mRNA 1 290 \&. + \&. ID=mRNA2;Parent=gene1
+seq gt csa exon 1 90 \&. + \&. Parent=mRNA2
+seq gt csa exon 101 190 \&. + \&. Parent=mRNA2
+seq gt csa exon 201 290 \&. + \&. Parent=mRNA2
+###
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+As one can see, they have been combined into a consensus spliced alignment (represented as genes with mRNAs as children which in turn have exons as children) with two alternative splice forms\&. The first and the third spliced alignment have been combined into the first alternative splice form (mRNA1) and the the second and the fourth spliced alignment into the second alternative splice form (mRNA2)\&.
+.sp
+As one can see, the second exon from the first alternative splice form ist shorter than the corresponding exon from the second alternative splice form\&.
+.SH "AUTHOR"
+.sp
+Report bugs to <gt\-users at genometools\&.org>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1 2012-10-10 19:34:52 UTC (rev 12373)
+++ trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1 2012-10-10 22:20:53 UTC (rev 12374)
@@ -2,12 +2,12 @@
.\" Title: gt-fingerprint
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 10/07/2012
+.\" Date: 10/10/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-FINGERPRINT" "1" "10/07/2012" "\ \&" "\ \&"
+.TH "GT\-FINGERPRINT" "1" "10/10/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -86,26 +86,77 @@
.SH "DESCRIPTION"
.sp
If neither option \-check nor option \-duplicates is used, the fingerprints for all sequences are shown on stdout\&.
-.SH "EXAMPLES:"
.sp
+Examples:
+.sp
Compute (unified) list of fingerprints:
.sp
+.if n \{\
+.RS 4
+.\}
+.nf
$ gt fingerprint U89959_ests\&.fas | sort | uniq > U89959_ests\&.checklist_uniq
+.fi
+.if n \{\
+.RE
+.\}
.sp
Compare fingerprints:
.sp
-$ gt fingerprint \-check U89959_ests\&.checklist_uniq U89959_ests\&.fas 950b7715ab6cc030a8c810a0dba2dd33 only in sequence_file(s)
+.if n \{\
+.RS 4
+.\}
+.nf
+$ gt fingerprint \-check U89959_ests\&.checklist_uniq U89959_ests\&.fas
+950b7715ab6cc030a8c810a0dba2dd33 only in sequence_file(s)
+.fi
+.if n \{\
+.RE
+.\}
.sp
Make sure a sequence file contains no duplicates (not the case here):
.sp
-$ gt fingerprint \-duplicates U89959_ests\&.fas 950b7715ab6cc030a8c810a0dba2dd33 2 gt fingerprint: error: duplicates found: 1 out of 200 (0\&.500%)
+.if n \{\
+.RS 4
+.\}
+.nf
+$ gt fingerprint \-duplicates U89959_ests\&.fas
+950b7715ab6cc030a8c810a0dba2dd33 2
+gt fingerprint: error: duplicates found: 1 out of 200 (0\&.500%)
+.fi
+.if n \{\
+.RE
+.\}
.sp
Extract sequence with given fingerprint:
.sp
-$ gt fingerprint \-extract 6d3b4b9db4531cda588528f2c69c0a57 U89959_ests\&.fas >SQ;8720010 TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTTACATGATACCAACGTAATG GGAGCTTAAAAATA
-.SH "RETURN VALUES:"
+.if n \{\
+.RS 4
+.\}
+.nf
+$ gt fingerprint \-extract 6d3b4b9db4531cda588528f2c69c0a57 U89959_ests\&.fas
+>SQ;8720010
+TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTTACATGATACCAACGTAATG
+GGAGCTTAAAAATA
+.fi
+.if n \{\
+.RE
+.\}
.sp
-0 everything went fine (\-check: the comparison was successful; \-duplicates: no duplicates found) 1 an error occured (\-check: the comparison was not successful; \-duplicates: duplicates found)
+Return values:
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+0 everything went fine (\-check: the comparison was successful;
+ \-duplicates: no duplicates found)
+1 an error occured (\-check: the comparison was not successful;
+ \-duplicates: duplicates found)
+.fi
+.if n \{\
+.RE
+.\}
.SH "AUTHOR"
.sp
Report bugs to <gt\-users at genometools\&.org>\&.
Modified: trunk/packages/genometools/trunk/debian/man/gt-hop.1
===================================================================
--- trunk/packages/genometools/trunk/debian/man/gt-hop.1 2012-10-10 19:34:52 UTC (rev 12373)
+++ trunk/packages/genometools/trunk/debian/man/gt-hop.1 2012-10-10 22:20:53 UTC (rev 12374)
@@ -2,12 +2,12 @@
.\" Title: gt-hop
.\" Author: [see the "AUTHOR" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 10/07/2012
+.\" Date: 10/10/2012
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
-.TH "GT\-HOP" "1" "10/07/2012" "\ \&" "\ \&"
+.TH "GT\-HOP" "1" "10/10/2012" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -71,7 +71,7 @@
.PP
\fB\-reads\fR
.RS 4
-uncorrected read file(s) in FastQ format; the corrected reads are output in the currect working directory in files which are named as the input files, each prepended by a prefix (see \-outprefix option) \-reads allows to output the reads in the same order as in the input and is mandatory if the SAM contains more than a single primary alignment for each read (e\&.g\&. output of bwasw) see also \-o option as an alternative
+uncorrected read file(s) in FastQ format; the corrected reads are output in the currect working directory in files which are named as the input files, each prepended by a prefix (see \-outprefix option) \-reads allows one to output the reads in the same order as in the input and is mandatory if the SAM contains more than a single primary alignment for each read (e\&.g\&. output of bwasw) see also \-o option as an alternative
.RE
.PP
\fB\-outprefix\fR
@@ -131,7 +131,7 @@
.sp
The aggressive mode tries to maximize the sensitivity, the conservative mode to minimize the false positives\&. An even more conservative set of corrections can be achieved using the \-ann option (see \-help+)\&.
.sp
-The \-expert mode allows to manually set each parameter; the default values are the same as in the \-conservative mode\&.
+The \-expert mode allows one to manually set each parameter; the default values are the same as in the \-conservative mode\&.
.sp
(Finally, for evaluation purposes only, the \-state\-of\-truth mode can be used: this mode assumes that the target sequence of the sequencing has been specified as reference sequence and outputs an ideal list of corrections\&.)
.SH "AUTHOR"
Modified: trunk/packages/genometools/trunk/debian/rules
===================================================================
--- trunk/packages/genometools/trunk/debian/rules 2012-10-10 19:34:52 UTC (rev 12373)
+++ trunk/packages/genometools/trunk/debian/rules 2012-10-10 22:20:53 UTC (rev 12374)
@@ -3,6 +3,7 @@
#export DH_VERBOSE=1
export DESTDIR=$(CURDIR)/debian/tmp
+export DH_ALWAYS_EXCLUDE=.gitignore
BITS:=$(shell dpkg-architecture | grep DEB_BUILD_ARCH_BITS | cut -f 2 -d'=')
ifeq ($(BITS),64)
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