[med-svn] r250 - trunk/packages/sigma-align/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Sat Apr 7 06:44:15 UTC 2007
Author: charles-guest
Date: 2007-04-07 06:44:15 +0000 (Sat, 07 Apr 2007)
New Revision: 250
Modified:
trunk/packages/sigma-align/trunk/debian/changelog
trunk/packages/sigma-align/trunk/debian/sigma.1.xml
Log:
manpage enhanced by Upstream
Modified: trunk/packages/sigma-align/trunk/debian/changelog
===================================================================
--- trunk/packages/sigma-align/trunk/debian/changelog 2007-04-07 06:42:23 UTC (rev 249)
+++ trunk/packages/sigma-align/trunk/debian/changelog 2007-04-07 06:44:15 UTC (rev 250)
@@ -1,12 +1,7 @@
-sigma-align (1.1-1) UNRELEASED; urgency=low
+sigma-align (1.1-1) unstable; urgency=low
- * (NOT RELEASED YET) New upstream release
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 7 Apr 2007 15:36:27 +0900
-
-sigma-align (1.0-2) unstable; urgency=low
-
- * Enhancing manpage with quotes from the website.
+ * New upstream release.
+ * Manpage enhanced by the upstream author of sigma.
* Add Subversion repository URL to debian/control.
-- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 4 Mar 2007 22:54:45 +0900
Modified: trunk/packages/sigma-align/trunk/debian/sigma.1.xml
===================================================================
--- trunk/packages/sigma-align/trunk/debian/sigma.1.xml 2007-04-07 06:42:23 UTC (rev 249)
+++ trunk/packages/sigma-align/trunk/debian/sigma.1.xml 2007-04-07 06:44:15 UTC (rev 250)
@@ -71,52 +71,84 @@
<variablelist>
<varlistentry>
- <term><option>-A</option>
+ <term><option>-A</option>, <option>--aligned_output</option>
</term>
<listitem>
- <para>Aligned output (compare with <option>-F</option> option) (default: only this).</para>
+ <para>Aligned, pretty-printed output (compare
+ with <option>-F</option> option) (default: only this). See
+ also <option>-C</option>.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-b</option>
+ <term><option>-b</option>, <option>--bgprobfile</option>
<parameter>filename</parameter>
</term>
<listitem>
- <para>Auxiliary file from which to read background sequences (overridden by <option>-B</option>).</para>
+ <para>Auxiliary file (in fasta format) from which to read
+ background sequences (overridden by <option>-B</option>).
+ Typically this is a file containing large quantities of
+ similar non-coding sequence, from which background
+ probabilities of single- and di-nucleotides may be estimated.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
- <option>-B</option>
+ <option>-B</option>, <option>--bgseqfile</option>
<parameter>filename</parameter>
</term>
<listitem>
- <para>File containing background probabilities.</para>
+ <para>File containing background probabilities. The format
+ is described further below.
</listitem>
</varlistentry>
+ <varlistentry>
+ <term><option>-C</option></term>, <option>--caps_only</option>
+ <listitem>
+ <para>Use only upper-case letters in output sequence, for
+ compatibility with output of some other programs like
+ ClustalW and MLagan. By default, output is mixed-case (as
+ in Dialign), and lower-case bases are treated as not
+ aligned.
+ </para>
+ </listitem>
+ </varlistentry>
+
<varlistentry>
- <term><option>-F</option>
+ <term><option>-F</option>, <option>--fasta_output</option>
</term>
<listitem>
- <para>Fasta output (can use both <option>-A</option> and <option>-F</option> in either order).</para>
+ <para>Multi-fasta output (can use both <option>-A</option>
+ and <option>-F</option> in either order). See also <option>-C</option>.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-n</option>
+ <term><option>-l</option>, <option>--maxfraglength</option>
<parameter>number</parameter>
</term>
<listitem>
+ <para>Pre-fragment very long sequences into pieces of this
+ average length, for efficiency. Default = 4000. Smaller =
+ faster and more memory-efficient, larger may be better.
+ </listitem>
+ </varlistentry>
+
+
+ <varlistentry>
+ <term><option>-n</option>, <option>--ncorrel</option>
+ <parameter>number</parameter>
+ </term>
+ <listitem>
<para>Background correlation (default <parameter>2</parameter>=dinucleotide;
<parameter>1</parameter>=single-site basecounts, <parameter>0</parameter>=0.25 per base).</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-x</option>
+ <term><option>-x</option>, <option>--significance</option>
<parameter>number</parameter>
</term>
<listitem>
@@ -126,7 +158,7 @@
</varlistentry>
<varlistentry>
- <term><option>-help</option>,
+ <term><option>-h</option>,
<option>--help</option>
</term>
<listitem>
@@ -145,7 +177,13 @@
Using a <quote>background model</quote> appropriate to the sequences being aligned greatly reduces spurious alignments on synthetic data (and, one hopes, on real data too). The simplest way to ensure this is to supply, via the <option>-b</option> parameter, a FASTA-format file containing large quantities of similar sequence data (eg, if one is aligning yeast sequences, supply a file containing all intergenic yeast sequence).
</para>
<para>
- Instead of this, if the single-site and dinucleotide frequencies are known already, they may be supplied in a file via the -B option. The file format should be: one entry per line, with the mononucleotide or dinucleotide (case-insensitive) followed by the frequency. (eg, "A 0.3", "AT 0.16", etc on successive lines.) A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored).
+ Instead of this, if the single-site and dinucleotide frequencies
+ are known already, they may be supplied in a file via the -B
+ option. The file format should be: one entry per line, with the
+ mononucleotide or dinucleotide (case-insensitive) followed by
+ the frequency. (eg, "A 0.3", "AT 0.16", etc on successive
+ lines.) A sample file is in the "Background" subdirectory of the
+ source distribution. A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored).
</para>
</refsect1>
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