Docs update #5

docs/build/html/_sources/index.rst.txt

@@ -37,6 +37,16 @@ Currently, ``SPECIMEN`` includes the following pipelines (for a summary refer to
     <img src='_images/hqtb.png' alt='HQTB' title='HQTB' style="width: 30%;">
   </a>
 
+.. image:: images/buttons/PGAB_constr.png
+  :height: 0px
+  :width: 0px
+
+.. raw:: html
+
+  <a class="reference external image-reference" href="pipeline_idea.html">
+    <img src='_images/PGAB_constr.png' alt='PGAB' title='PGAB' style="width: 30%;">
+  </a>
+
 .. toctree::
    :maxdepth: 2
    :caption: Content

docs/build/html/_sources/overview-pipes.rst.txt

@@ -36,4 +36,12 @@ a similar organism to the one the new model should be curated for.
 
     About HQTB <hqtb/about-pipeline>
     Run HQTB <hqtb/run-pipeline>
-    HQTB Configuration <hqtb/hqtb-config>
+    HQTB Configuration <hqtb/hqtb-config>
+
+More ideas for pipelines
+------------------------
+
+Below are some ideas for pipelines, which may be implemented in future update(s):
+
+.. toctree::
+    pgap based <pipeline_idea>

docs/build/html/_sources/pipeline_idea.rst.txt

@@ -0,0 +1,38 @@
+PGAB: From genome sequence to draft model
+=========================================
+
+PGAB: PGAP based pipeline
+
+.. note::
+
+    This pipeline is still in the idea stage and will be object to a future update.
+
+Generating a model for an organism where no information on genes and proteins is obtainable via any database 
+causes the problem that the model will not contain valid database identifiers for any GeneProduct. To resolve this issue the 
+workflow in Figure :numref:`workflow` can be used.
+
+1. First annotate the genome with NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) to obtain the same FASTA format as used in NCBI and use the flag for taxonomy checking.
+2. Then use DIAMOND with the ``nr`` database from NCBI and the obtained annotated FASTA file as input. Restrict the search to your organism's taxon if known.
+3. Check if any protein in the annotation FASTA file still has no database identifier.
+
+    | -> YES: Rerun DIAMOND without the taxonomy check and without the restriction for the organism's taxon.
+    |
+    | -> NO: Continue with step 4.
+
+4. Add the DIAMOND result to the annotated FASTA file.
+5. Run e.g. ``CarveMe`` to obtain a draft model.
+6. Check if in the model any GeneProducts without NCBI Protein or RefSeq identifiers occur.
+
+    | -> YES: 
+    |     i. Use individual BLAST searches for the remaining GeneProducts.
+    |     ii. Add the results to the annotated and refined FASTA file.
+    |     iii. Create again a draft model with the same program with the newly refined FASTA file.
+    | 
+    | -> NO: The draft model is done.
+
+.. _workflow:
+
+.. figure:: images/genome2draft.svg
+  :alt: Workflow from genome sequence to a draft model
+
+  Workflow from genome sequence to a draft model

docs/build/html/hqtb/about-pipeline.html

@@ -65,6 +65,7 @@
 <li class="toctree-l3"><a class="reference internal" href="hqtb-config.html">HQTB Configuration</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="../overview-pipes.html#more-ideas-for-pipelines">More ideas for pipelines</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../specimen.html">Contents of SPECIMEN</a></li>

docs/build/html/hqtb/hqtb-config.html

@@ -27,7 +27,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Contents of SPECIMEN" href="../specimen.html" />
+    <link rel="next" title="PGAB: From genome sequence to draft model" href="../pipeline_idea.html" />
     <link rel="prev" title="Run the HTQB Pipeline" href="run-pipeline.html" /> 
 </head>
 
@@ -62,6 +62,7 @@
 <li class="toctree-l3 current"><a class="current reference internal" href="#">HQTB Configuration</a></li>
 </ul>
 </li>
+<li class="toctree-l2"><a class="reference internal" href="../overview-pipes.html#more-ideas-for-pipelines">More ideas for pipelines</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../specimen.html">Contents of SPECIMEN</a></li>
@@ -224,7 +225,7 @@ <h1>HQTB Configuration File<a class="headerlink" href="#hqtb-configuration-file"
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="run-pipeline.html" class="btn btn-neutral float-left" title="Run the HTQB Pipeline" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="../specimen.html" class="btn btn-neutral float-right" title="Contents of SPECIMEN" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="../pipeline_idea.html" class="btn btn-neutral float-right" title="PGAB: From genome sequence to draft model" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>