[med-svn] r1766 - trunk/packages/ncbi-epcr/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Wed Apr 16 11:02:02 UTC 2008
Author: tille
Date: 2008-04-16 11:02:01 +0000 (Wed, 16 Apr 2008)
New Revision: 1766
Added:
trunk/packages/ncbi-epcr/trunk/debian/famap.1
Modified:
trunk/packages/ncbi-epcr/trunk/debian/control
trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1
trunk/packages/ncbi-epcr/trunk/debian/fahash.1
trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1
Log:
Manpage for famap, fixed other manpages
Modified: trunk/packages/ncbi-epcr/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/control 2008-04-15 15:21:51 UTC (rev 1765)
+++ trunk/packages/ncbi-epcr/trunk/debian/control 2008-04-16 11:02:01 UTC (rev 1766)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 5.0), docbook-to-man, quilt, cdbs
+Build-Depends: debhelper (>= 5.0), quilt, cdbs
Standards-Version: 3.7.3
Homepage: http://www.ncbi.nlm.nih.gov/sutils/e-pcr/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-epcr/trunk/?rev=0&sc=0
Modified: trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1 2008-04-15 15:21:51 UTC (rev 1765)
+++ trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1 2008-04-16 11:02:01 UTC (rev 1766)
@@ -1,30 +1,30 @@
.TH "E-PCR" "1" "February 2004"
-.SH "NAME"
-e-PCR \(em Find sequence tagged sites (STS) in DNA sequences
-.SH "SYNOPSIS"
-.PP
-\fBe-PCR [-hV] [posix-options] stsfile [fasta ...]\fR [\fB\fIcompat-options\fR\fP]
-.SH "DESCRIPTION"
-.PP
+.SH "NAME"
+e-PCR \(em Find sequence tagged sites (STS) in DNA sequences
+.SH "SYNOPSIS"
+.PP
+\fBe-PCR [-hV] [posix-options] stsfile [fasta ...]\fR [\fB\fIcompat-options\fR\fP]
+.SH "DESCRIPTION"
+.PP
The program substitutes blast in the location of pairs primers on the
-genome that may yield a PCR product.
-
-.SH "OPTIONS"
+genome that may yield a PCR product.
+
+.SH "OPTIONS"
.PP
posix-options are:
-.IP "\fB-m=\fI##\fR\fP " 10
+.IP "\fB-m=\fI##\fR\fP " 10
Margin (default 50)
-.IP "\fB-w=\fI##\fR\fP " 10
+.IP "\fB-w=\fI##\fR\fP " 10
Wordsize (default 7)
-.IP "\fB-n=\fI##\fR\fP " 10
+.IP "\fB-n=\fI##\fR\fP " 10
Max mismatches allowed (default 0)
-.IP "\fB-g=\fI##\fR\fP " 10
+.IP "\fB-g=\fI##\fR\fP " 10
Max indels allowed (default 0)
-.IP "\fB-f=\fI##\fR\fP " 10
+.IP "\fB-f=\fI##\fR\fP " 10
Use ## discontiguos words, slow if ##>1
-.IP "\fB-o=\fI##\fR\fP " 10
+.IP "\fB-o=\fI##\fR\fP " 10
Set output file
-.IP "\fB-t=\fI##\fR\fP " 10
+.IP "\fB-t=\fI##\fR\fP " 10
Set output format:
.IP "" 10
1 - classic, range (pos1..pos2)
@@ -34,73 +34,73 @@
3 - tabular
.IP "" 10
4 - tabular with alignment in comments (slow)
-.IP "\fB-d=\fI##-##\fR\fP " 10
+.IP "\fB-d=\fI##-##\fR\fP " 10
Set default size range (default 100-350)
-.IP "\fB-p=\fI+-\fR\fP " 10
+.IP "\fB-p=\fI+-\fR\fP " 10
Turn hits postprocess on/off
-.IP "\fB-v=\fI##\fR\fP " 10
+.IP "\fB-v=\fI##\fR\fP " 10
Verbosity flags
-.IP "\fB-a=\fIa|f\fR\fP " 10
+.IP "\fB-a=\fIa|f\fR\fP " 10
Use presize alignmens (only if gaps>0), slow
.IP "" 10
a - Allways or f - as Fallback
-.IP "\fB-x=\fI+-\fR\fP " 10
+.IP "\fB-x=\fI+-\fR\fP " 10
Use 5'-end lowercase masking of primers (default -)
-.IP "\fB-u=\fI+-\fR\fP " 10
+.IP "\fB-u=\fI+-\fR\fP " 10
Uppercase all primers (default -)
.P
compat-options (duplicate posix-options) are
-.IP "\fBM=\fI##\fR\fP " 10
-Margin (default 50)
-.IP "\fBW=\fI##\fR\fP " 10
+.IP "\fBM=\fI##\fR\fP " 10
+Margin (default 50)
+.IP "\fBW=\fI##\fR\fP " 10
Wordsize (default 7)
-.IP "\fBN=\fI##\fR\fP " 10
+.IP "\fBN=\fI##\fR\fP " 10
Number of mismatches allowed (default 0)
-.IP "\fBG=\fI##\fR\fP " 10
+.IP "\fBG=\fI##\fR\fP " 10
Max indels allowed (default 0)
-.IP "\fBF=\fI##\fR\fP " 10
+.IP "\fBF=\fI##\fR\fP " 10
Use ## discontinuos words
-.IP "\fBO=\fI##\fR\fP " 10
+.IP "\fBO=\fI##\fR\fP " 10
Set output file to ##
-.IP "\fBT=\fI##\fR\fP " 10
+.IP "\fBT=\fI##\fR\fP " 10
Set output format (1..3)
-.IP "\fBD=\fI##-##\fR\fP " 10
+.IP "\fBD=\fI##-##\fR\fP " 10
Set default size range
-.IP "\fBP=\fI+-\fR\fP " 10
+.IP "\fBP=\fI+-\fR\fP " 10
Postprocess hits on/off
-.IP "\fBV=\fI##\fR\fP " 10
+.IP "\fBV=\fI##\fR\fP " 10
Verbosity flags
-.IP "\fBA=\fIa|f\fR\fP " 10
+.IP "\fBA=\fIa|f\fR\fP " 10
Use presize alignmens (only if gaps>0), slow
.IP "" 10
a - Allways or f - as Fallback
-.IP "\fBX=\fI+-\fR\fP " 10
+.IP "\fBX=\fI+-\fR\fP " 10
Use 5'-end lowercase masking of primers (default -)
-.IP "\fBU=\fI+-\fR\fP " 10
+.IP "\fBU=\fI+-\fR\fP " 10
Uppercase all primers (default -)
-.IP "\fB-mid\fP " 10
+.IP "\fB-mid\fP " 10
Same as T=2
.P
For information about further options just call \fBe-PCR\fR
without any options.
-.SH "SEE ALSO"
-.PP
+.SH "SEE ALSO"
+.PP
+/usr/share/doc/ncbi-epcr/README.txt
+.PP
bioperl(1), re-pcr(1)
-.PP
-/usr/share/doc/ncbi-epcr
-.PP
+.PP
.SH "AUTHORS"
-.PP
+.PP
This manual page was written by Steffen Moeller <moeller at debian.org>
-and Andreas Tille <tille at debian.org> for
-the \fBDebian\fP system (but may be used by others). Permission is
-granted to copy, distribute and/or modify this document under
-the terms of the GNU General Public License, Version 2 any
-later version published by the Free Software Foundation.
-
-.PP
-On Debian systems, the complete text of the GNU General Public
-License can be found in /usr/share/common-licenses/GPL.
+and Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
Modified: trunk/packages/ncbi-epcr/trunk/debian/fahash.1
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/fahash.1 2008-04-15 15:21:51 UTC (rev 1765)
+++ trunk/packages/ncbi-epcr/trunk/debian/fahash.1 2008-04-16 11:02:01 UTC (rev 1766)
@@ -1,11 +1,20 @@
-.TH FAHASH "1" "April 2008"
+.TH FAHASH "1" "April 2008" "Reverse e-PCR: sequence hash builder version 2.3.9" "User Commands"
.SH NAME
-fahash \- build hash-file, and output word usage statistics for re-PCR
-.SH DESCRIPTION
+fahash \- sequence hash builder for reverse e-PCR
+
+.SH SYNOPSIS
fahash [\-hV] \fB\-b\fR hash\-file [\-w wdsize] [\-f period] [\-F fragment_min,fragment_max] [\-k] [\-c cachesize] [\-v 1|2] famap\-file ...
.PP
fahash [\-hV] \fB\-T\fR hash\-file [\-o outfile]
-.SS "where:"
+
+.SH DESCRIPTION
+
+The program
+.B fahash
+is part of the e-PCR suite and is used to build hash-files,
+and output word usage statistics for reverse e-PCR searches.
+
+.SH OPTIONS
.TP
\fB\-b\fR hash\-file
Build hash tables (hash\-file) from sequence files,
@@ -36,20 +45,31 @@
\fB\-v\fR ver
Use format version (1|2, 2 is default)
-.SH "SEE ALSO"
-.PP
-bioperl(1), e-pcr(1), re-pcr(1)
-.PP
-/usr/share/doc/ncbi-epcr
-.PP
+.SH "EXAMPLE"
+
+.PP
+ famap -tN -b genome.famap org/chr_*.fa
+.PP
+ fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
+.PP
+ re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
+
+See famap(1) and re-pcr(1)
+
+.SH "SEE ALSO"
+.PP
+/usr/share/doc/ncbi-epcr/README.txt
+.PP
+bioperl(1), e-pcr(1), famap(1) and re-pcr(1)
+.PP
.SH "AUTHORS"
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> for
-the \fBDebian\fP system (but may be used by others). Permission is
-granted to copy, distribute and/or modify this document under
-the terms of the GNU General Public License, Version 2 any
-later version published by the Free Software Foundation.
-
-.PP
-On Debian systems, the complete text of the GNU General Public
-License can be found in /usr/share/common-licenses/GPL.
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
Added: trunk/packages/ncbi-epcr/trunk/debian/famap.1
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/famap.1 (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/famap.1 2008-04-16 11:02:01 UTC (rev 1766)
@@ -0,0 +1,60 @@
+.TH FASTA "1" "April 2008" "Fasta converter for e-PCR version 2.3.9" "User Commands"
+.SH NAME
+famap \- prepare Fasta sequence database for re-PCR searches
+
+.SH SYNOPSIS
+famap [\-hV] \fB\-b\fR mmapped\-file [\-t cvt] [fafile ...]
+.PP
+famap [\-hV] \fB\-d\fR mmapped\-file [ord ...]
+.PP
+famap [\-hV] \fB\-l\fR mmapped\-file [ord ...]
+
+.SH DESCRIPTION
+
+The program
+.B famap
+is part of the e-PCR suite and is used to build mmapped-file from
+FASTA files for reverse e-PCR searches
+
+.SH OPTIONS
+where cvt (convertion table) is one of:
+.IP
+off \- as is (default)
+.IP
+n \- nucleotide [acgtnACGTN] allowed,
+.IP
+N \- nucleotide uppercase allowed [ACGTN]
+.IP
+nx \- nucleotide with ambiquity codes allowed
+.IP
+NX \- nucleotide with ambiquity codes uppercase
+
+
+.SH "EXAMPLE"
+
+.PP
+ famap -tN -b genome.famap org/chr_*.fa
+.PP
+ fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
+.PP
+ re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
+
+See famap(1) and re-pcr(1)
+
+.SH "SEE ALSO"
+.PP
+/usr/share/doc/ncbi-epcr/README.txt
+.PP
+bioperl(1), e-pcr(1), famap(1) and re-pcr(1)
+.PP
+.SH "AUTHORS"
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
Modified: trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1 2008-04-15 15:21:51 UTC (rev 1765)
+++ trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1 2008-04-16 11:02:01 UTC (rev 1766)
@@ -1,22 +1,23 @@
.TH "RE-PCR" "1" "April 2008"
-.SH "NAME"
-re-PCR \(em Find sequence tagged sites (STS) in DNA sequences
-.SH "SYNOPSIS"
-.PP
-\fBre-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]
+.SH "NAME"
+re-PCR \(em Find sequence tagged sites (STS) in DNA sequences
+.SH "SYNOPSIS"
+.PP
+.B re-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]
-\fBre-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]
+.B re-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]
-\fBre-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]
+.B re-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]
-\fBre-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]
+.B re-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]
-.SH "DESCRIPTION"
+.SH "DESCRIPTION"
.PP
Implements reverse searching (called Reverse e-PCR) to make it feasible
-to search the human genome sequence and other large genomes.
-
-.SH "OPTIONS"
+to search the human genome sequence and other large genomes by
+performing STS and primer searches.
+
+.SH "OPTIONS"
.PP
.IP "\fB-p=\fIhash-file\fR\fP " 10
Perform primer lookup using hash-file
@@ -49,21 +50,31 @@
.IP "\fB-q\fP " 10
Quiet (no progress indicator)
+.SH "EXAMPLE"
-.SH "SEE ALSO"
-.PP
-bioperl(1), e-pcr(1)
-.PP
-/usr/share/doc/ncbi-epcr
-.PP
+.PP
+ famap -tN -b genome.famap org/chr_*.fa
+.PP
+ fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
+.PP
+ re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
+
+See famap(1) and fahash(1)
+
+.SH "SEE ALSO"
+.PP
+/usr/share/doc/ncbi-epcr/README.txt
+.PP
+bioperl(1), e-pcr(1), famap(1) and fahash(1)
+.PP
.SH "AUTHORS"
-.PP
-This manual page was written by Andreas Tille <tille at debian.org> for
-the \fBDebian\fP system (but may be used by others). Permission is
-granted to copy, distribute and/or modify this document under
-the terms of the GNU General Public License, Version 2 any
-later version published by the Free Software Foundation.
-
-.PP
-On Debian systems, the complete text of the GNU General Public
-License can be found in /usr/share/common-licenses/GPL.
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
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