diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index bb6d26da2c4741822d40696fdb00b138912a939a..3dbaa167988aa86ca28af6b8d50f335559b92b8f 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -59,6 +59,41 @@
<span class="kn">import</span> <span class="nn">argparse</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">gzip</span>
+<span class="kn">import</span> <span class="nn">tempfile</span>
+
+<span class="kn">import</span> <span class="nn">ost</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
+
+<span class="k">def</span> <span class="nf">_AssembleTrgTplAln</span><span class="p">(</span><span class="n">target</span><span class="p">,</span> <span class="n">template</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Internal function: Assemble a target-template alignment without leading/</span>
+<span class="sd"> final gaps in the target sequence. Set the offset for the template sequence.</span>
+<span class="sd"> """</span>
+ <span class="c"># count leading gaps to get the start position</span>
+ <span class="n">start</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">target</span><span class="o">.</span><span class="n">length</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">target</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'-'</span><span class="p">:</span>
+ <span class="n">start</span> <span class="o">=</span> <span class="n">i</span>
+ <span class="k">break</span>
+ <span class="c"># get rid of closing gaps at the end</span>
+ <span class="n">end</span> <span class="o">=</span> <span class="n">target</span><span class="o">.</span><span class="n">length</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">target</span><span class="o">.</span><span class="n">length</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">target</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'-'</span><span class="p">:</span>
+ <span class="n">end</span> <span class="o">=</span> <span class="n">i</span>
+ <span class="k">break</span>
+ <span class="c"># assemble template sequence</span>
+ <span class="n">tpl_str</span> <span class="o">=</span> <span class="s">''</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">start</span><span class="p">,</span> <span class="n">end</span><span class="p">):</span>
+ <span class="n">tpl_str</span> <span class="o">+=</span> <span class="n">template</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">new_aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="n">target</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">target</span><span class="p">)[</span><span class="n">start</span><span class="p">:</span><span class="n">end</span><span class="p">]),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="n">template</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
+ <span class="n">tpl_str</span><span class="p">))</span>
+ <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceOffset</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">start</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">new_aln</span>
<div class="viewcode-block" id="PM3ArgumentParser"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser">[docs]</a><span class="k">class</span> <span class="nc">PM3ArgumentParser</span><span class="p">(</span><span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -66,7 +101,7 @@
<span class="sd"> set of standard arguments which can be activated, rather than added via the</span>
<span class="sd"> traditional way. This helps keeping up a common naming scheme throughout</span>
<span class="sd"> all |project| actions. As a real extension, this subclass provides checking</span>
-<span class="sd"> of input parameters on :meth:`~pm3argparse.PM3ArgumentParser.Parse`. Beside</span>
+<span class="sd"> of input parameters on :meth:`Parse`. Beside</span>
<span class="sd"> this, everything you can do with a 'real' :class:`~argparse.ArgumentParser`</span>
<span class="sd"> instance is possible here.</span>
@@ -108,27 +143,210 @@
<span class="n">formatter_class</span><span class="o">=</span>\
<span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentDefaultsHelpFormatter</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">action</span> <span class="o">=</span> <span class="n">action</span>
-
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
</div>
-<div class="viewcode-block" id="PM3ArgumentParser.Parse"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.Parse">[docs]</a> <span class="k">def</span> <span class="nf">Parse</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">namespace</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+ <span class="k">def</span> <span class="nf">_print_message</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+ <span class="c">#pylint: disable=redefined-builtin</span>
+ <span class="sd">"""</span>
+<span class="sd"> This is like a welcome message to the "country of bad style"... we are</span>
+<span class="sd"> overwriting a "_" function from the parent-class. Those guys should not</span>
+<span class="sd"> be used outside of the housing module, never... but here it is a single</span>
+<span class="sd"> function to bend :mod:`argparse` to use :class:`ost.Logger`.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">message</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">file</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="nb">file</span> <span class="ow">is</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">:</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+
+<div class="viewcode-block" id="PM3ArgumentParser.Parse"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.Parse">[docs]</a> <span class="k">def</span> <span class="nf">Parse</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Parse an argument string.</span>
<span class="sd"> :param args: The argument string. As default |sysargv|_ is used.</span>
<span class="sd"> :type args: :class:`list`</span>
-<span class="sd"> :param namespace: The same as for</span>
-<span class="sd"> :meth:`argparse.ArgumentParser.parse_args`.</span>
-
-<span class="sd"> :returns: If :attr:`namespace` is not given,</span>
-<span class="sd"> :class:`argparse.Namespace`.</span>
+<span class="sd"> :returns: :class:`promod3.cor.pm3argparse.PM3OptionsNamespace`.</span>
<span class="sd"> """</span>
- <span class="n">opts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">parse_args</span><span class="p">(</span><span class="n">args</span><span class="o">=</span><span class="n">args</span><span class="p">,</span> <span class="n">namespace</span><span class="o">=</span><span class="n">namespace</span><span class="p">)</span>
+ <span class="n">opts</span> <span class="o">=</span> <span class="n">PM3OptionsNamespace</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">parse_args</span><span class="p">(</span><span class="n">args</span><span class="o">=</span><span class="n">args</span><span class="p">,</span> <span class="n">namespace</span><span class="o">=</span><span class="n">opts</span><span class="p">)</span>
+
+ <span class="n">opts</span><span class="o">.</span><span class="n">PostProcess</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
<span class="k">return</span> <span class="n">opts</span>
+</div>
+<div class="viewcode-block" id="PM3ArgumentParser.AssembleParser"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">[docs]</a> <span class="k">def</span> <span class="nf">AssembleParser</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> When adding options via the :meth:`Add*` methods, call this after you</span>
+<span class="sd"> are done. Everything before just tells the parser that it should</span>
+<span class="sd"> contain those option sets but does not actually add anything.</span>
+<span class="sd"> :meth:`AssembleParser` will put everything in place, in the right order</span>
+<span class="sd"> and with the right constraints.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="s">'ALIGNMENT'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleAlignment</span><span class="p">()</span>
+</div>
+<div class="viewcode-block" id="PM3ArgumentParser.AddAlignment"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">[docs]</a> <span class="k">def</span> <span class="nf">AddAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Add everything needed to load alignments to the argument parser. Creates</span>
+<span class="sd"> several options/ arguments and adds some checks for post processing.</span>
+<span class="sd"> This method only adds a flag to the parser to add alignment options on</span>
+<span class="sd"> :meth:`AssembleParser`. Depending on which options you activate, things</span>
+<span class="sd"> need to be added in a different order or have other constraints.</span>
+
+<span class="sd"> Options/ arguments added:</span>
+
+<span class="sd"> * ``--fasta trg:<NAME> <FILE>`` - describing a target-template alignment</span>
+<span class="sd"> with ``trg:`` marking the target sequence inside :file:`<FILE>`</span>
+
+<span class="sd"> Exit codes related to alignment input:</span>
+
+<span class="sd"> * 11 - no prefix ``trg:`` found for an argument to '--fasta'</span>
+
+<span class="sd"> * 12 - a given alignment file does not exist</span>
+
+<span class="sd"> * 13 - never raised (parameter for checking gzip files)</span>
+
+<span class="sd"> * 14 - empty target name found (``trg:``)</span>
+
+<span class="sd"> * 15 - found an empty alignment file</span>
+
+<span class="sd"> * 16 - alignment with more than 2 sequences found</span>
+
+<span class="sd"> * 17 - target sequence name not found in alignment</span>
+
+<span class="sd"> * 18 - sequences in the alignment have different length</span>
+
+<span class="sd"> Attributes added to the namespace returned by</span>
+<span class="sd"> :meth:`Parse`:</span>
+
+<span class="sd"> * :attr:`fasta` - filled with the input of the '--fasta' argument, a</span>
+<span class="sd"> :class:`list` with multiple :class:`list` objects</span>
+
+<span class="sd"> * :attr:`alignments` - :class:`ost.AlignmentList`, same order as</span>
+<span class="sd"> :attr:`fasta`</span>
+
+<span class="sd"> * :attr:`aln_sources` - the original source of the alignment, may be</span>
+<span class="sd"> filename(s) or a string in JSON format,</span>
+<span class="sd"> :class:`list` of all sources</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">[</span><span class="s">'ALIGNMENT'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+</div>
+ <span class="k">def</span> <span class="nf">_AssembleAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Actually add alignment arguments/ options</span>
+<span class="sd"> """</span>
+ <span class="c"># FastA input: - always pairwise alignments</span>
+ <span class="c"># - callable multiple times</span>
+ <span class="c"># - goes by 'trg:<SEQNAME> <FILE>'</span>
+ <span class="c"># - excludes JSON file/ object</span>
+ <span class="c"># - leading whitespaces will be deleted</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'-f'</span><span class="p">,</span> <span class="s">'--fasta'</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s">'append'</span><span class="p">,</span>
+ <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s">'trg:<NAME>'</span><span class="p">,</span> <span class="s">'<FILE>'</span><span class="p">),</span>
+ <span class="n">help</span><span class="o">=</span><span class="s">'Pairwise alignment in FastA format, needs to '</span><span class="o">+</span>
+ <span class="s">'declare what is the target sequence.'</span><span class="p">)</span>
+ <span class="c"># input: FastA/ JSON</span>
+ <span class="c"># determined by extension: if we are wrong, the whole loading fails</span>
+ <span class="c"># possibility to add JSON: mention limitation!</span>
+</div>
+<span class="k">class</span> <span class="nc">PM3OptionsNamespace</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> This one is mainly for internal use. You can use it like everything that</span>
+<span class="sd"> comes out of :meth:`argparse.ArgumentParser.parse_args`. Attributes are</span>
+<span class="sd"> added regarding how you assembled your argument parser.</span>
+<span class="sd"> """</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">pass</span>
+
+ <span class="k">def</span> <span class="nf">PostProcess</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">activated</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Post processing of activated option packs.</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="s">'ALIGNMENT'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_PostProcessAlignment</span><span class="p">()</span>
+
+ <span class="k">def</span> <span class="nf">_PostProcessAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c">#pylint: disable=no-member</span>
+ <span class="c">#pylint: disable=attribute-defined-outside-init</span>
+ <span class="sd">"""</span>
+<span class="sd"> Doing some extra work after parsing.</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aln_sources</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">alignments</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">AlignmentList</span><span class="p">()</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">fasta</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fasta</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">src</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">'trg:'</span><span class="p">):</span>
+ <span class="n">trgname</span> <span class="o">=</span> <span class="n">src</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">4</span><span class="p">:]</span>
+ <span class="n">seqfile</span> <span class="o">=</span> <span class="n">src</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">elif</span> <span class="n">src</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">'trg:'</span><span class="p">):</span>
+ <span class="n">trgname</span> <span class="o">=</span> <span class="n">src</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">4</span><span class="p">:]</span>
+ <span class="n">seqfile</span> <span class="o">=</span> <span class="n">src</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--fasta' requires one argument "</span><span class="o">+</span>
+ <span class="s">"prefixed with 'trg:' marking the "</span><span class="o">+</span>
+ <span class="s">"target sequence name"</span><span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">trgname</span><span class="p">):</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--fasta' requires argument "</span><span class="o">+</span>
+ <span class="s">"'trg:' defining the "</span><span class="o">+</span>
+ <span class="s">"target sequence name, empty one "</span><span class="o">+</span>
+ <span class="s">"found: '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">src</span><span class="p">),</span> <span class="mi">14</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s">"Alignment"</span><span class="p">,</span> <span class="mi">12</span><span class="p">,</span> <span class="n">seqfile</span><span class="p">)</span>
+ <span class="n">is_gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileGzip</span><span class="p">(</span><span class="s">"Alignment"</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="n">seqfile</span><span class="p">)</span>
+ <span class="n">readfile</span> <span class="o">=</span> <span class="n">seqfile</span>
+ <span class="k">if</span> <span class="n">is_gz</span><span class="p">:</span>
+ <span class="n">zip_fh</span> <span class="o">=</span> <span class="n">gzip</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">seqfile</span><span class="p">)</span>
+ <span class="n">unzip_str</span> <span class="o">=</span> <span class="n">zip_fh</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
+ <span class="n">zip_fh</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="n">unzip_file</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">NamedTemporaryFile</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s">'w'</span><span class="p">,</span>
+ <span class="n">suffix</span><span class="o">=</span><span class="s">'.fas'</span><span class="p">)</span>
+ <span class="n">unzip_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">unzip_str</span><span class="p">)</span>
+ <span class="n">unzip_file</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+ <span class="n">readfile</span> <span class="o">=</span> <span class="n">unzip_file</span><span class="o">.</span><span class="n">name</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">aln</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="n">readfile</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="s">"fasta"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span> <span class="c">#pylint: disable=broad-except</span>
+ <span class="k">if</span> <span class="n">exc</span><span class="o">.</span><span class="n">message</span> <span class="o">==</span> <span class="s">'Bad FASTA file: File is empty'</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--fasta' refers to an empty "</span><span class="o">+</span>\
+ <span class="s">"file or its in the wrong "</span><span class="o">+</span>
+ <span class="s">"format: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">seqfile</span><span class="p">,</span> <span class="mi">15</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">exc</span><span class="o">.</span><span class="n">message</span> <span class="o">==</span> <span class="s">'sequences have different lengths'</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--fasta </span><span class="si">%s</span><span class="s">': "</span> <span class="o">%</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">src</span><span class="p">)</span><span class="o">+</span>
+ <span class="s">"sequences in the alignment "</span><span class="o">+</span>
+ <span class="s">"have different length."</span><span class="p">,</span> <span class="mi">18</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span>
+ <span class="k">finally</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">is_gz</span><span class="p">:</span>
+ <span class="n">unzip_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="c"># check alignment</span>
+ <span class="n">nos</span> <span class="o">=</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetCount</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">nos</span> <span class="o">></span> <span class="mi">2</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--fasta </span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">src</span><span class="p">)</span><span class="o">+</span>
+ <span class="s">"points to an alignment with "</span><span class="o">+</span>
+ <span class="s">"more than 2 sequences."</span><span class="p">,</span> <span class="mi">16</span><span class="p">)</span>
+ <span class="n">fst_seq</span> <span class="o">=</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetSequence</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+ <span class="n">snd_seq</span> <span class="o">=</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetSequence</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">fst_seq</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="n">trgname</span><span class="p">:</span>
+ <span class="n">new_aln</span> <span class="o">=</span> <span class="n">_AssembleTrgTplAln</span><span class="p">(</span><span class="n">fst_seq</span><span class="p">,</span> <span class="n">snd_seq</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">snd_seq</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="n">trgname</span><span class="p">:</span>
+ <span class="n">new_aln</span> <span class="o">=</span> <span class="n">_AssembleTrgTplAln</span><span class="p">(</span><span class="n">snd_seq</span><span class="p">,</span> <span class="n">fst_seq</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--fasta </span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">src</span><span class="p">)</span><span class="o">+</span>
+ <span class="s">"does not define a target name "</span><span class="o">+</span>
+ <span class="s">"found in the alignment."</span><span class="p">,</span> <span class="mi">17</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">new_aln</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aln_sources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">seqfile</span><span class="p">)</span>
<span class="c"># LocalWords: param attr prog argparse ArgumentParser bool sys os init str</span>
<span class="c"># LocalWords: progattr descattr argpinit argv formatter meth args namespace</span>
-<span class="c"># LocalWords: ArgumentDefaultsHelpFormatter sysargv</span></div></div>
+<span class="c"># LocalWords: ArgumentDefaultsHelpFormatter sysargv AssembleParser fasta io</span>
+<span class="c"># LocalWords: metavar trg tpl FastA gzip tempfile ost promod aln stderr src</span>
+<span class="c"># LocalWords: AssembleTrgTplAln CreateSequence SetSequenceOffset LogError</span>
+<span class="c"># LocalWords: LogScript OptionsNamespace PostProcess AssembleAlignment JSON</span>
+<span class="c"># LocalWords: AddAlignment AlignmentList SEQNAME whitespaces nargs trgname</span>
+<span class="c"># LocalWords: PostProcessAlignment startswith seqfile elif MsgErrorAndExit</span>
+<span class="c"># LocalWords: len FileExists gz FileGzip readfile fh NamedTemporaryFile fas</span>
+<span class="c"># LocalWords: LoadAlignment exc GetCount fst GetSequence snd</span>
</pre></div>
</div>
diff --git a/doc/html/_sources/core/pm3argparse.txt b/doc/html/_sources/core/pm3argparse.txt
index 43e05c1265ae13d3092c52a3c8e30bfdde516afc..b787f1144335b62a4c102dab7464675678d1242e 100644
--- a/doc/html/_sources/core/pm3argparse.txt
+++ b/doc/html/_sources/core/pm3argparse.txt
@@ -13,9 +13,10 @@ arguments in common. For example we need an input alignment quite often and
usually for an alignment we need information on what is the target sequence,
what identifies a template sequence and eventually a hint on the format. That
means we need the same functionality on the command line in several actions.
-There :class:`pm3argparse.PM3ArgumentParser` serves as a simplification. It
-provides a set of standard arguments you just need to activate for your action
-plus it comes with some verification functionality for input.
+There :class:`~promod3.core.pm3argparse.PM3ArgumentParser` serves as a
+simplification. It provides a set of standard arguments you just need to
+activate for your action plus it comes with some verification functionality for
+input.
.. synopsis/ example
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index f5035485b5216c03ffa7596dc340d4f1011db805..c3c1ed5c7d9d98381d88398be26671e5bc576b4e 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -68,9 +68,10 @@ arguments in common. For example we need an input alignment quite often and
usually for an alignment we need information on what is the target sequence,
what identifies a template sequence and eventually a hint on the format. That
means we need the same functionality on the command line in several actions.
-There <code class="xref py py-class docutils literal"><span class="pre">pm3argparse.PM3ArgumentParser</span></code> serves as a simplification. It
-provides a set of standard arguments you just need to activate for your action
-plus it comes with some verification functionality for input.</p>
+There <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal"><span class="pre">PM3ArgumentParser</span></code></a> serves as a
+simplification. It provides a set of standard arguments you just need to
+activate for your action plus it comes with some verification functionality for
+input.</p>
</div>
<div class="section" id="argument-parser">
<h2>Argument Parser<a class="headerlink" href="#argument-parser" title="Permalink to this headline">¶</a></h2>
@@ -81,7 +82,7 @@ plus it comes with some verification functionality for input.</p>
set of standard arguments which can be activated, rather than added via the
traditional way. This helps keeping up a common naming scheme throughout
all ProMod3 actions. As a real extension, this subclass provides checking
-of input parameters on <code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code>. Beside
+of input parameters on <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>. Beside
this, everything you can do with a ‘real’ <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">ArgumentParser</span></code></a>
instance is possible here.</p>
<p>A note on exit codes: if <code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code> is
@@ -129,24 +130,76 @@ first 3 characters of the file name of the script. If
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">
+<code class="descname">AddAlignment</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.AddAlignment"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="Permalink to this definition">¶</a></dt>
+<dd><p>Add everything needed to load alignments to the argument parser. Creates
+several options/ arguments and adds some checks for post processing.
+This method only adds a flag to the parser to add alignment options on
+<a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a>. Depending on which options you activate, things
+need to be added in a different order or have other constraints.</p>
+<p>Options/ arguments added:</p>
+<ul class="simple">
+<li><code class="docutils literal"><span class="pre">--fasta</span> <span class="pre">trg:<NAME></span> <span class="pre"><FILE></span></code> - describing a target-template alignment
+with <code class="docutils literal"><span class="pre">trg:</span></code> marking the target sequence inside <code class="file docutils literal"><span class="pre"><FILE></span></code></li>
+</ul>
+<p>Exit codes related to alignment input:</p>
+<ul class="simple">
+<li>11 - no prefix <code class="docutils literal"><span class="pre">trg:</span></code> found for an argument to ‘–fasta’</li>
+<li>12 - a given alignment file does not exist</li>
+<li>13 - never raised (parameter for checking gzip files)</li>
+<li>14 - empty target name found (<code class="docutils literal"><span class="pre">trg:</span></code>)</li>
+<li>15 - found an empty alignment file</li>
+<li>16 - alignment with more than 2 sequences found</li>
+<li>17 - target sequence name not found in alignment</li>
+<li>18 - sequences in the alignment have different length</li>
+</ul>
+<p>Attributes added to the namespace returned by
+<a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
+<ul>
+<li><dl class="first docutils">
+<dt><code class="xref py py-attr docutils literal"><span class="pre">fasta</span></code> - filled with the input of the ‘–fasta’ argument, a</dt>
+<dd><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> with multiple <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> objects</p>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt><code class="xref py py-attr docutils literal"><span class="pre">alignments</span></code> - <code class="xref py py-class docutils literal"><span class="pre">ost.AlignmentList</span></code>, same order as</dt>
+<dd><p class="first last"><code class="xref py py-attr docutils literal"><span class="pre">fasta</span></code></p>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt><code class="xref py py-attr docutils literal"><span class="pre">aln_sources</span></code> - the original source of the alignment, may be</dt>
+<dd><p class="first last">filename(s) or a string in JSON format,
+<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of all sources</p>
+</dd>
+</dl>
+</li>
+</ul>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">
+<code class="descname">AssembleParser</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.AssembleParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="Permalink to this definition">¶</a></dt>
+<dd><p>When adding options via the <code class="xref py py-meth docutils literal"><span class="pre">Add*()</span></code> methods, call this after you
+are done. Everything before just tells the parser that it should
+contain those option sets but does not actually add anything.
+<a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal"><span class="pre">AssembleParser()</span></code></a> will put everything in place, in the right order
+and with the right constraints.</p>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.Parse">
-<code class="descname">Parse</code><span class="sig-paren">(</span><em>args=None</em>, <em>namespace=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.Parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Parse</code><span class="sig-paren">(</span><em>args=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.Parse"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="Permalink to this definition">¶</a></dt>
<dd><p>Parse an argument string.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>args</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – The argument string. As default <a class="reference external" href="https://docs.python.org/2.7/library/sys.html#sys.argv"><code class="xref py py-attr docutils literal"><span class="pre">sys.argv</span></code></a> is used.</li>
-<li><strong>namespace</strong> – The same as for
-<a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.ArgumentParser.parse_args" title="(in Python v2.7)"><code class="xref py py-meth docutils literal"><span class="pre">argparse.ArgumentParser.parse_args()</span></code></a>.</li>
-</ul>
-</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – The argument string. As default <a class="reference external" href="https://docs.python.org/2.7/library/sys.html#sys.argv"><code class="xref py py-attr docutils literal"><span class="pre">sys.argv</span></code></a> is used.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">If <code class="xref py py-attr docutils literal"><span class="pre">namespace</span></code> is not given,
-<a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.Namespace" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">argparse.Namespace</span></code></a>.</p>
-</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">promod3.cor.pm3argparse.PM3OptionsNamespace</span></code>.</td>
</tr>
</tbody>
</table>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index c2b808b91e0350723ae5c6374feb7c3e1f7ba635..d53636a956ff9a11027dfb087325003083d64b85 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -87,8 +87,6 @@
<dt><a href="actions/index_dev.html#test_actions.ActionTestCase">ActionTestCase (class in test_actions)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt>
add_doc_dependency
@@ -100,6 +98,8 @@
</dt>
</dl></dd>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt>
add_doc_source
@@ -111,6 +111,14 @@
</dt>
</dl></dd>
+
+ <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">AddAlignment() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+ </dt>
+
+
+ <dt><a href="core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">AssembleParser() (promod3.core.pm3argparse.PM3ArgumentParser method)</a>
+ </dt>
+
</dl></td>
</tr></table>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 97e919fbb3e76fc22fd69ebca7e0532a5eca0d82..ad1430b780a7f4b55305827d498f096c72aa3440 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index cf991d0c7654bc363532cf4140fa1b4aea4b026e..b25dbdce6aa89985a8d78e74fd0269d19183ed39 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:46,filenames:["actions/index_dev","buildsystem","changelog","cmake/index","contributing","core/helper","core/index","core/pm3argparse","core/setcompoundschemlib","developers","index","rawmodel/index","users"],objects:{"":{"command:add_doc_dependency":[3,0,1,""],"command:add_doc_source":[3,0,1,""],"command:pm_action":[3,0,1,""],"command:promod3_unittest":[3,0,1,""],test_actions:[0,1,0,"-"]},"promod3.core":{pm3argparse:[7,1,0,"-"]},"promod3.core.helper":{FileExists:[5,2,1,""],FileExtension:[5,2,1,""],FileGzip:[5,2,1,""],MsgErrorAndExit:[5,2,1,""]},"promod3.core.pm3argparse":{PM3ArgumentParser:[7,5,1,""]},"promod3.core.pm3argparse.PM3ArgumentParser":{"__init__":[7,3,1,""],Parse:[7,3,1,""],action:[7,4,1,""]},"promod3.rawmodel":{BuildRawModel:[11,2,1,""],RawModelingResult:[11,5,1,""]},"promod3.rawmodel.RawModelingResult":{gaps:[11,4,1,""],model:[11,4,1,""]},"test_actions.ActionTestCase":{RunAction:[0,3,1,""],RunExitStatusTest:[0,3,1,""],pm_action:[0,4,1,""],pm_bin:[0,4,1,""],testPMExists:[0,3,1,""]},promod3:{SetCompoundsChemlib:[8,2,1,""],core:[6,1,0,"-"],rawmodel:[11,1,0,"-"]},test_actions:{ActionTestCase:[0,5,1,""]}},objnames:{"0":["cmake","command","CMake 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