[med-svn] r5032 - trunk/packages/acedb/trunk/debian

Sun Jul 11 05:11:56 UTC 2010

Author: moeller
Date: 2010-07-11 05:11:55 +0000 (Sun, 11 Jul 2010)
New Revision: 5032

Added:
   trunk/packages/acedb/trunk/debian/dotter.1
   trunk/packages/acedb/trunk/debian/efetch.1
Log:
Who did not check in my newly created man pages?


Added: trunk/packages/acedb/trunk/debian/dotter.1
===================================================================

--- trunk/packages/acedb/trunk/debian/dotter.1	                        (rev 0)
+++ trunk/packages/acedb/trunk/debian/dotter.1	2010-07-11 05:11:55 UTC (rev 5032)
@@ -0,0 +1,79 @@
+.\" This file was generated by help2man 1.37.1 and then manually edited.
+.TH DOTTER: "1" "July 2010" 
+.SH NAME
+dotter \- Sequence dotplots with image enhancement tools.
+.SH SYNOPSIS
+dotter [options] <horizontal_sequence> <vertical_sequence> [X options]
+.SH DESCRIPTION
+.IP
+Reference: Sonnhammer ELL & Durbin R (1995). A dot\-matrix program
+with dynamic threshold control suited for genomic DNA and protein
+sequence analysis. Gene 167(2):GC1\-10.
+.TP
+.TP
+Allowed types:
+Protein        \-      Protein
+DNA            \-      DNA
+DNA            \-      Protein
+.IP
+Options:
+.TP
+\fB\-b\fR <file>
+Batch mode, write dotplot to <file>
+.TP
+\fB\-l\fR <file>
+Load dotplot from <file>
+.TP
+\fB\-m\fR <float>
+Memory usage limit in Mb (default 0.5)
+.TP
+\fB\-z\fR <int>
+Set zoom (compression) factor
+.TP
+\fB\-p\fR <int>
+Set pixel factor manually (ratio pixelvalue/score)
+.TP
+\fB\-W\fR <int>
+Set sliding window size. (K => Karlin/Altschul estimate)
+.TP
+\fB\-M\fR <file>
+Read in score matrix from <file> (Blast format; Default: Blosum62).
+.TP
+\fB\-F\fR <file>
+Read in sequences and data from <file> (replaces sequencefiles).
+.TP
+\fB\-f\fR <file>
+Read feature segments from <file>
+.TP
+\fB\-H\fR
+Do not calculate dotplot at startup.
+.TP
+\fB\-R\fR
+Reversed Greyramp tool at start.
+.TP
+\fB\-r\fR
+Reverse and complement horizontal_sequence (DNA vs Protein)
+.TP
+\fB\-D\fR
+Don't display mirror image in self comparisons
+.TP
+\fB\-w\fR
+For DNA: horizontal_sequence top strand only (Watson)
+.TP
+\fB\-c\fR
+For DNA: horizontal_sequence bottom strand only (Crick)
+.TP
+\fB\-q\fR <int>
+Horizontal_sequence offset
+.TP
+\fB\-s\fR <int>
+Vertical_sequence offset
+.IP
+Some X options:
+\fB\-acefont\fR <font> Main font.
+\fB\-font\fR    <font> Menu font.
+.SH SEE ALSO
+http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html for more info.
+.SH AUTHOR
+Erik.Sonnhammer at cgb.ki.se
+Version 3.1, compiled Jul 10 2010

Added: trunk/packages/acedb/trunk/debian/efetch.1
===================================================================
--- trunk/packages/acedb/trunk/debian/efetch.1	                        (rev 0)
+++ trunk/packages/acedb/trunk/debian/efetch.1	2010-07-11 05:11:55 UTC (rev 5032)
@@ -0,0 +1,95 @@
+.\" This file was generated by help2man 1.37.1 with some additional
+.\" manual editing.
+.TH EFETCH "1" "July 2010" 
+.SH NAME
+efetch \- retrieve entries from sequence databases.
+.SH SYNOPSIS
+efetch \fB\-options\fR [database:]<query>
+.SH DESCRIPTION
+In the late 90s efetch was a very popular tool to extremely quickly retrieve 
+entried from the most common public bioinformatics sequence and motif databases.
+We will learn from the Debian and Ubuntu popularity contest effort if the
+package is possibly gaining a larger userbase again.
+.SH DATABASES
+SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite
+.SH OPTIONS:
+\fB\-a\fR            Search with Accession number
+.HP
+\fB\-f\fR            Fasta format output
+.HP
+\fB\-q\fR            Sequence only output (one line)
+.HP
+\fB\-s\fR <#>        Start at position #
+.HP
+\fB\-e\fR <#>        Stop at position #
+.HP
+\fB\-o\fR            More options and info...
+.HP
+\fB\-D\fR <dir>
+Specify database directory
+.HP
+\fB\-H\fR
+Display index header data
+.HP
+\fB\-p\fR
+Display entrynames in search path
+.HP
+\fB\-r\fR
+Print sequence in 'raw' format
+.HP
+\fB\-m\fR
+Fetch from mixed mini database
+.HP
+\fB\-M\fR
+Mini format output
+.HP
+\fB\-b\fR
+Do NOT reverse the order of bytes
+(SunOS, IRIX do reverse, Alpha not)
+.HP
+\fB\-d\fR <dbfile>
+Specify database file (avoid this)
+.HP
+\fB\-i\fR <idxfile>
+Specify index file (avoid this)
+.HP
+\fB\-l\fR <divfile>
+Specify division lookup table (avoid this)
+.HP
+\fB\-B\fR <database> Specify database (archaic)
+.HP
+\fB\-A\fR
+Only return entryname for accession number
+.HP
+\fB\-n\fR <name>
+Give the sequence this name
+.HP
+\fB\-x\fR
+Don't require query to match entry's name exactly (avoid)
+.HP
+\fB\-w\fR
+For Wormpep: also fetch cross\-referenced SwissProt entry
+.HP
+\fB\-h\fR
+shows this help text
+.SH ENVIRONMENT
+SWDIR      = SwissProt  directory \- database and EMBL index files
+PIRDIR     = PIR        \fB\-\-\fR " \fB\-\-\fR
+WORMDIR    = Wormpep    \fB\-\-\fR " \fB\-\-\fR
+EMBLDIR    = EMBL       \fB\-\-\fR " \fB\-\-\fR
+GBDIR      = Genbank    \fB\-\-\fR " \fB\-\-\fR
+PRODOMDIR  = ProDom     \fB\-\-\fR " \fB\-\-\fR
+PROSITEDIR = ProSite    \fB\-\-\fR " \fB\-\-\fR
+DBDIR      = User's own \fB\-\-\fR " \fB\-\-\fR (fasta format)
+.TP
+SEQDB
+database file (default SwissProt)
+.IP
+SEQDBIDX index file
+DIVTABL  division lookup table
+.IP
+Ex. setenv DBDIR /pubseq/seqlibs/embl/
+.IP
+Note that Prodom family consensus seqs can be fetched by PD:_#
+.SH AUTHOR
+Erik Sonnhammer (esr at sanger.ac.uk)


