Bug fixes for new factoring

docs/source/commands.rst

@@ -165,7 +165,7 @@ Run metagenomic reads against a succesfully built database. See :doc:`Tutorial 2
 
 .. code-block:: console
 
-    $ expam run -db DB_NAME [args...]
+    $ expam classify -db DB_NAME [args...]
 
 .. option:: -d <file path>, --directory <file path>
 
@@ -226,7 +226,7 @@ Run metagenomic reads against a succesfully built database. See :doc:`Tutorial 2
 
         .. code-block:: console
 
-            $ expam run ... --group #FF0000 sample_one sample_two
+            $ expam classify ... --group #FF0000 sample_one sample_two
 
 .. option:: --alpha <float>
 
@@ -260,7 +260,7 @@ Example
 
 .. code-block:: console
 
-    $ expam run -db DB_NAME -d /path/to/paired/reads --paired --out ~/paired_reads_analysis --taxonomy
+    $ expam classify -db DB_NAME -d /path/to/paired/reads --paired --out ~/paired_reads_analysis --taxonomy
 
 .. _download taxonomy:
 
@@ -305,7 +305,7 @@ Translate phylogenetic classification output to NCBI taxonomy.
 Plotting results on phylotree
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Results are automatically visualised on top of a phylogenetic tree when during the :code:`expam run` command,
+Results are automatically visualised on top of a phylogenetic tree when during the :code:`expam classify` command,
 but can also be done after classification using the :code:`phylotree` command.
 
 .. code-block::
@@ -393,7 +393,7 @@ Example
 .. note::
 
     The :code:`expam_limit` context works the same for any command. :code:`expam build`
-    can be replaced with :code:`expam run`, or any other command.
+    can be replaced with :code:`expam classify`, or any other command.
 
 The following is an example of the (tab-separated) log file output:
 

docs/source/tree.rst

@@ -3,27 +3,27 @@
 
 A programmatic API to interact with phylogenetic trees, particularly those used in reference databases.
 
-expam.tree.Location
--------------------
+expam.tree.location.Location
+----------------------------
 
-.. autoclass:: expam.tree.Location
+.. autoclass:: expam.tree.location.Location
 
-.. autofunction:: expam.tree.Location.__init__
+.. autofunction:: expam.tree.location.Location.__init__
 
-expam.tree.Index
-----------------
+expam.tree.tree.Index
+---------------------
 
-.. autoclass:: expam.tree.Index
+.. autoclass:: expam.tree.tree.Index
 
-.. autofunction:: expam.tree.Index.load_newick
+.. autofunction:: expam.tree.tree.Index.load_newick
 
-.. autofunction:: expam.tree.Index.from_newick
+.. autofunction:: expam.tree.tree.Index.from_newick
 
     Example loading an Index object from a Newick string.
 
     .. code-block:: python
 
-        >>> from expam.tree import Index
+        >>> from expam.tree.tree import Index
         >>> tree_string = "(B:6.0,(A:5.0,C:3.0,E:4.0):5.0,D:11.0);"
         >>> leaves, index = Index.from_newick(tree_string)
         * Initialising node pool...
@@ -42,13 +42,13 @@ expam.tree.Index
         >>> index['A'].coordinate
         [0, 0, 1, 0]
 
-.. autofunction:: expam.tree.Index.resolve_polytomies
+.. autofunction:: expam.tree.tree.Index.resolve_polytomies
 
-.. autofunction:: expam.tree.Index.coord
+.. autofunction:: expam.tree.tree.Index.coord
 
-.. autofunction:: expam.tree.Index.to_newick
+.. autofunction:: expam.tree.tree.Index.to_newick
 
-.. autofunction:: expam.tree.Index.yield_child_nodes
+.. autofunction:: expam.tree.tree.Index.yield_child_nodes
 
     .. code-block:: python
 
@@ -70,9 +70,9 @@ expam.tree.Index
         Internal node (branch) names can start with 'p', but this may also be neglected.
 
 
-.. autofunction:: expam.tree.Index.yield_leaves
+.. autofunction:: expam.tree.tree.Index.yield_leaves
 
-.. autofunction:: expam.tree.Index.get_child_nodes
+.. autofunction:: expam.tree.tree.Index.get_child_nodes
 
     .. code-block:: python
 
@@ -81,4 +81,4 @@ expam.tree.Index
         >>> index.get_child_nodes('E')
         ['E']
 
-.. autofunction:: expam.tree.Index.get_child_leaves
+.. autofunction:: expam.tree.tree.Index.get_child_leaves

docs/source/tutorials/classify.rst

@@ -93,7 +93,7 @@ Phylogenetic classification results
 
   .. code-block:: console
 
-    $ expam run -db my_database -d /path/to/sample_one.fq --out sample_one
+    $ expam classify -db my_database -d /path/to/sample_one.fq --out sample_one
 
 * In :code:`./sample_one`, there will be a :code:`phy` subdirectory containing three files:
 
@@ -199,11 +199,11 @@ Taxonomic results
 
 .. code-block:: console
 
-  $ expam run -d /path/to/reads --out example --taxonomy
+  $ expam classify -d /path/to/reads --out example --taxonomy
 
 .. code-block:: console
 
-  $ expam run -d /path/to/reads --out example_one
+  $ expam classify -d /path/to/reads --out example_one
   $ expam to_taxonomy --out example_one
 
 * Where before the results directory contained only a :code:`phy` subdirectory, it will now also contain a :code:`tax` folder.

docs/source/tutorials/graphical.rst

 Graphical output
 ================
 
-* When a :code:`run` or :code:`to_taxonomy` command is executed, raw summary files are produced (as described in :doc:`Classification <classify>`) and a phylotree is also produced as a graphical depiction of the sample summary.
+* When a :code:`classify` or :code:`to_taxonomy` command is executed, raw summary files are produced (as described in :doc:`Classification <classify>`) and a phylotree is also produced as a graphical depiction of the sample summary.
 * This graphical representation has some customisable features:
   
   * Multiple samples can be plotted on the same tree, with different colours for different samples.
@@ -61,8 +61,8 @@ Example of grouping
 
 .. code-block:: console
 
-    $ expam run ... --group a1 a2 a3 --group b1 b2 b3
-    $ expam run ... --group "#FF0000" a1 a2 a3 --group "#00FF00" b1 b2 b3
+    $ expam classify ... --group a1 a2 a3 --group b1 b2 b3
+    $ expam classify ... --group "#FF0000" a1 a2 a3 --group "#00FF00" b1 b2 b3
 
 .. note:: 
 
@@ -82,7 +82,7 @@ Example of grouping
 
     .. code-block:: console
 
-        $ expam run ... --paired --group a1_f a2_f --group b1_f b2_f
+        $ expam classify ... --paired --group a1_f a2_f --group b1_f b2_f
 
 Visual flags
 ^^^^^^^^^^^^
@@ -110,7 +110,7 @@ Example of colour list
 
 .. code-block:: console
 
-    $ expam run ... --colour_list "#FF0000" "#00FF00" "#0000FF"
+    $ expam classify ... --colour_list "#FF0000" "#00FF00" "#0000FF"
 
 
 .. _itol integration:
@@ -126,7 +126,7 @@ folder containing two files:
 * :code:`tree.nwk` - Newick format tree that can be inserted into iTOL.
 * :code:`style.txt` - An iTOL formatted text document that contains all the information needed for iTOL to style the tree.
 
-For instance, say we previously ran :code:`expam run --out my_run -d /some/samples`, and 
+For instance, say we previously ran :code:`expam classify --out my_run -d /some/samples`, and 
 now run :code:`expam phylotree --out my_run --itol`, the corresponding files
 would be located at
 

docs/source/tutorials/quickstart.rst

@@ -97,7 +97,7 @@ Running classifications
   
     * :code:`../expam/test/data/reads/`
   
-* We use the :code:`run` command to classify reads.
+* We use the :code:`classify` command to classify reads.
 * These are paired reads, but for now we'll treat them as separate.
 * We supply the :code:`-o` or :code:`--out` flag to tell *expam* where to save classification results.
 
@@ -105,7 +105,7 @@ Running classifications
 
 .. code-block:: console
     
-    $ expam run -db test -d /Users/seansolari/Documents/expam/test/data/reads/ --out test/results/unpaired_test
+    $ expam classify -db test -d /Users/seansolari/Documents/expam/test/data/reads/ --out test/results/unpaired_test
     Clearing old log files...
     Results directory created at /Users/seansolari/Documents/Databases/test/results/unpaired_test.
     Loading the map and phylogeny.
@@ -202,7 +202,7 @@ Running paired data
 
 .. code-block:: console
 
-    $ expam run -db test -d /Users/seansolari/Documents/expam/test/data/reads/ --out test/results/paired_test --paired
+    $ expam classify -db test -d /Users/seansolari/Documents/expam/test/data/reads/ --out test/results/paired_test --paired
     Clearing old log files...
     Results directory created at /Users/seansolari/Documents/Databases/test/results/paired_test.
     Loading the map and phylogeny.

src/expam/classify/classify.py

@@ -99,13 +99,10 @@ def run_classifier(
         if taxonomy:
             # Attempt to update taxon ids.
             tax_obj: TaxonomyNCBI = TaxonomyNCBI(database_config)
-            tax_obj.accession_to_taxonomy(db_dir)
+            tax_obj.accession_to_taxonomy()
 
-            tax_results_path = os.path.join(out_dir, output_config.tax)
-            os.mkdir(output_config.tax)
-
-            name_to_lineage, taxon_to_rank = tax_obj.load_taxonomy_map(db_dir)
-            results.to_taxonomy(name_to_lineage, taxon_to_rank, tax_results_path)
+            name_to_lineage, taxon_to_rank = tax_obj.load_taxonomy_map()
+            results.to_taxonomy(name_to_lineage, taxon_to_rank)
 
         results.draw_results(itol_mode=itol_mode)
     finally:
@@ -469,7 +466,7 @@ class ClassificationResults:
         self.tax_id_hierarchy = {"1": set()}  # Map from tax_id -> immediate children.
         self.tax_id_pool = ["1"]  # Children must appear later than parent this list.
 
-    def to_taxonomy(self, name_to_lineage, taxon_to_rank, tax_dir):
+    def to_taxonomy(self, name_to_lineage, taxon_to_rank):
         col_names = ["c_perc", "c_cumul", "c_count", "s_perc", "s_cumul", "s_count", "rank", "scientific name"]
 
         class_counts = pd.read_csv(self.results_config.phy_classified, sep="\t", index_col=0, header=0)
@@ -544,7 +541,7 @@ class ClassificationResults:
             cutoff = max(self.cutoff, (total_counts / 1e6) * self.cpm)
             df = df[(df['c_cumul'] > cutoff) | (df['s_cumul'] > cutoff) | (df.index == 'unclassified')]
 
-            df.to_csv(os.path.join(tax_dir, sample_name + ".csv"), sep="\t", header=True)
+            df.to_csv(os.path.join(self.results_config.tax, sample_name + ".csv"), sep="\t", header=True)
 
             #
             # Map raw read output to taxonomy.

src/expam/cli/main.py

@@ -7,7 +7,7 @@ import shutil
 import matplotlib.pyplot as plt
 import numpy as np
 
-from expam.utils import die, ls, make_path_absolute
+from expam.utils import die, ls, make_path_absolute, parse_float, parse_int
 
 
 ExpamOptions = namedtuple(
@@ -166,42 +166,19 @@ class CommandGroup:
         except AttributeError:
             raise AttributeError("Command %s not found!" % command)
 
-    @staticmethod
-    def parse_ints(*params):
-        for param in params:
-            INVALID_PARAM_MSG = ("Invalid parameter (%s), must be integer!" % str(param))
-
-            if param is not None:
-
-                try:
-                    # Convert to float.
-                    param = float(param)
-
-                except ValueError:
-                    die(INVALID_PARAM_MSG)
-
-                # Convert to int and see if the value changes.
-                new_param = int(param)
-                if new_param != param:
-                    die(INVALID_PARAM_MSG)
-
-                param = new_param
-
-            yield param
-
-    @staticmethod
-    def parse_floats(*params):
-        for param in params:
-            INVALID_PARAM_MSG = ("Invalid parameter (%s), must be integer!" % str(param))
-
-            if param is not None:
-                try:
-                    param = float(param)
-
-                except ValueError:
-                    die(INVALID_PARAM_MSG)
+    @classmethod
+    def parse_ints(cls, *params):
+        if len(params) == 1:
+            return parse_int(params[0])
+        else:
+            return (parse_int(param) for param in params)
 
-            yield param
+    @classmethod
+    def parse_floats(cls, *params):
+        if len(params) == 1:
+            return parse_float(params[0])
+        else:
+            return (parse_float(param) for param in params)
 
     @staticmethod
     def get_user_confirmation(msg):

src/expam/tree/tree.py

@@ -8,7 +8,6 @@ import traceback
 import numpy as np
 import pandas as pd
 from expam.tree import PHYLA_COLOURS
-
 from expam.tree.location import Location
 
 

src/expam/utils.py

@@ -80,3 +80,31 @@ def is_hex(string):
 
     return True
 
+def parse_int(param):
+    INVALID_PARAM_MSG = ("Invalid parameter (%s), must be integer!" % str(param))
+    if param is not None:
+        try:
+            # Convert to float.
+            param = float(param)
+        except ValueError:
+            die(INVALID_PARAM_MSG)
+
+        # Convert to int and see if the value changes.
+        new_param = int(param)
+        if new_param != param:
+            die(INVALID_PARAM_MSG)
+    else:
+        new_param = None
+
+    return new_param
+
+def parse_float(param):
+    INVALID_PARAM_MSG = ("Invalid parameter (%s), must be integer!" % str(param))
+    if param is not None:
+        try:
+            param = float(param)
+        except ValueError:
+            die(INVALID_PARAM_MSG)
+
+    return param
+