Merge pull request #12 from rouskinlab/0.15.0

0.15.0

docs/_sources/api/seismicrna.cluster.rst.txt

@@ -6,6 +6,14 @@ seismicrna.cluster package
    :undoc-members:
    :show-inheritance:
 
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   seismicrna.cluster.tests
+
 Submodules
 ----------
 

docs/_sources/api/seismicrna.cluster.tests.rst.txt

@@ -0,0 +1,16 @@
+seismicrna.cluster.tests package
+================================
+
+.. automodule:: seismicrna.cluster.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.cluster.tests.em_test
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_sources/api/seismicrna.core.batch.rst.txt

@@ -6,6 +6,14 @@ seismicrna.core.batch package
    :undoc-members:
    :show-inheritance:
 
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   seismicrna.core.batch.tests
+
 Submodules
 ----------
 

docs/_sources/api/seismicrna.core.batch.tests.rst.txt

@@ -0,0 +1,22 @@
+seismicrna.core.batch.tests package
+===================================
+
+.. automodule:: seismicrna.core.batch.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.batch.tests.count_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.batch.tests.index_test
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_sources/api/seismicrna.core.mu.rst.txt

@@ -13,7 +13,6 @@ Subpackages
    :maxdepth: 4
 
    seismicrna.core.mu.tests
-   seismicrna.core.mu.unbias
 
 Submodules
 ----------
@@ -47,3 +46,9 @@ Submodules
    :members:
    :undoc-members:
    :show-inheritance:
+
+
+.. automodule:: seismicrna.core.mu.unbias
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_sources/api/seismicrna.core.mu.tests.rst.txt

@@ -38,3 +38,9 @@ Submodules
    :members:
    :undoc-members:
    :show-inheritance:
+
+
+.. automodule:: seismicrna.core.mu.tests.unbias_test
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_sources/api/seismicrna.core.rst.txt

@@ -34,6 +34,12 @@ Submodules
    :show-inheritance:
 
 
+.. automodule:: seismicrna.core.dims
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: seismicrna.core.header
    :members:
    :undoc-members:

docs/_sources/api/seismicrna.core.tests.rst.txt

@@ -10,6 +10,12 @@ Submodules
 ----------
 
 
+.. automodule:: seismicrna.core.tests.dims_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: seismicrna.core.tests.header_test
    :members:
    :undoc-members:

docs/_sources/api/seismicrna.relate.rst.txt

@@ -15,6 +15,7 @@ Subpackages
    seismicrna.relate.aux
    seismicrna.relate.c
    seismicrna.relate.py
+   seismicrna.relate.tests
 
 Submodules
 ----------
@@ -56,6 +57,12 @@ Submodules
    :show-inheritance:
 
 
+.. automodule:: seismicrna.relate.sim
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: seismicrna.relate.write
    :members:
    :undoc-members:

docs/_sources/api/seismicrna.relate.tests.rst.txt

@@ -0,0 +1,16 @@
+seismicrna.relate.tests package
+===============================
+
+.. automodule:: seismicrna.relate.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.relate.tests.sim_test
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_sources/howto/run/cluster.rst.txt

@@ -11,17 +11,14 @@ Cluster input file: Mask report
 You can give any number of Mask report files as inputs for the Cluster step.
 See :doc:`../inputs` for ways to list multiple files.
 
-For example, to cluster relation vectors of reads from ``sample-1`` masked over
-reference ``ref-1`` section ``abc``, and from ``sample-2`` masked over reference
-``ref-2`` section ``full``, use the command ::
+Cluster all masked reads in ``out``::
 
-    seismic cluster {out}/sample-1/mask/ref-1/abc {out}/sample-2/mask/ref-2/full
+    seismic cluster out
 
-where ``{out}`` is the path of your output directory from the Relate step.
+Cluster reads from ``sample-1`` masked over reference reference ``ref-1``,
+section ``abc``::
 
-To cluster all masked relation vectors in ``{out}``, you can use the command ::
-
-    seismic cluster {out}
+    seismic cluster out/sample-1/mask/ref-1/abc
 
 Cluster: Settings
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -105,9 +102,7 @@ You can set the number of independent EM runs using ``--em-runs`` (``-e``).
 Cluster: Output files
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-All output files go into the directory ``{out}/{sample}/cluster/{ref}/{sect}``,
-where ``{out}`` is the output directory, ``{sample}`` is the sample, ``{ref}``
-is the reference, and ``{sect}`` is the section.
+All output files go into the directory ``OUT/SAMPLE/cluster/REFERENCE/SECTION``.
 
 Cluster output file: Batch of cluster memberships
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -171,7 +166,7 @@ In your cluster report:
   If all runs converged to identical solutions, then every NRMSD would be 0 and
   every Correlation would be 1.
   Generally, the runs are sufficiently reproducible if runs 1 and 2 have NRMSDs
-  less than 0.1 and Correlations greater than 0.95 with respect to run 0.
+  less than 0.05 and Correlations greater than 0.98 with respect to run 0.
   If not, then there you have no evidence that run 0 is the global optimum for
   that number of clusters, so it would be best to rerun clustering using more
   independent runs to increase the chances of finding the global optimum.

docs/_sources/howto/run/mask.rst.txt

@@ -110,20 +110,27 @@ Mask setting: Filter reads
 The second substep of masking is filtering reads.
 You can filter reads based on three criteria, in this order:
 
+Filter reads by number of positions covering the section
+''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
+
+You can require every read to contain a minimum number of bases in the section
+(i.e. set a minimum coverage) using ``--min-ncov-read`` followed by the minimum
+coverage.
+The minimum coverage must be at least 1 because reads that do not cover the
+section at all should always be filtered out.
+Note that this filter considers only positions that were not pre-excluded (see
+:ref:`mask_exclude`).
+
 Filter reads by fraction of informative positions
 ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
 
-For some applications, such as finding alternative structures, every read must
-span the vast majority of positions in the section of the reference.
-You can set a limit on the minimum number of informative bases in the read,
-as a fraction of the number of non-excluded positions in the section, using
-``--min-finfo-read {f}``.
-For example, to require 95% of the non-excluded positions in the section to be
+You can set a limit on the minimum information in each read, as a fraction of
+the number of non-excluded positions in the read, using ``--min-finfo-read``
+followed by the minimum fraction of informative positions.
+For example, to require 95% of the non-excluded positions in the read to be
 informative, use ``--min-finfo-read 0.95``.
-If the section had 296 positions, and 141 remained after excluding positions
-(see :ref:`mask_exclude`), then a read with 137 informative positions would
-have an informed fraction of 97% and be kept, but a read with 133 informative
-positions would have an informed fraction of 94% and be discarded.
+Note that the denominator of this fraction is the number of bases in the read
+that cover the section; it is not just the length of the section or of the read.
 
 Filter reads by fraction of mutated positions
 ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''