Updated READMEs for package, Blast, Manager, Cookies.

OrthoEvol/Cookies/README.md

@@ -1,22 +1,26 @@
-Cookies Documentation
-======================
-For this project/package, we recommend using cookiecutter (along with Flask)
+# Cookies Documentation
+
+For this package, we recommend using cookiecutter (along with Flask or Dash which is built with Flask)
 to set up your directory if you intend to create a web app/interface for your project.
 
-Cookies makes it very easy to do this.
+`Cookies` makes it very easy to do this.
 
 Learn more about the [cookiecutter](https://github.com/audreyr/cookiecutter) package.
 
 ## Examples
+
 The [Manager module](https://github.com/datasnakes/OrthoEvolution/tree/master/OrthoEvol/Manager)
 uses the _CookBook_ and _Oven_ classes as a primary means of functioning.
 
-### Simple Implementation
+### A Simple Implementation
 
 ```python
 from OrthoEvol.Cookies import Oven
 
-Kitchen = Oven(repo="repo", user="user", project="project", output_dir="project_path")
+Kitchen = Oven(repo="repo", user="username", project="project-name",
+               output_dir="path/to/project")
 Pantry = Kitchen.Ingredients
-Kitchen.bake_the_*()
-```
+
+# To create a user directory
+Kitchen.bake_the_user()
+```

OrthoEvol/Manager/README.md

@@ -59,5 +59,4 @@ dd.dispatch(dd.strategies, dd.dispatcher, dd.configuration)
 
 ## Notes
 
-Please view our [BioSQL documentation](https://github.com/datasnakes/OrthoEvolution/tree/master/OrthoEvol/Manager/BioSQL/README.md) and view some of the
-static/config related [files](https://github.com/datasnakes/OrthoEvolution/tree/master/OrthoEvol/Manager/config/).
+Please view our [BioSQL documentation](https://github.com/datasnakes/OrthoEvolution/tree/master/OrthoEvol/Manager/BioSQL/README.md) and view some of the static/config related [files](https://github.com/datasnakes/OrthoEvolution/tree/master/OrthoEvol/Manager/config/).

OrthoEvol/Orthologs/Blast/README.md

@@ -30,30 +30,26 @@ Before you use this function, you need for `NCBI Blast+` to be installed and in
 Download the latest standalone blast executables from
 [here](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/). We are currently using version `2.8.1`.
 
-
 #### Our Blast Methods
 
 NCBI's `blastn` can be configured (using its parameters) in a number of different ways 
-(for local or remote use or with seqidlists or taxids). For typical orthology analyses, 
+(i.e. local or remote use and with seqidlists or taxids). For typical orthology analyses, 
 it's important to take advantage of the speed and efficiency of NCBI's newest 
 preformatted blast databases ([blastdbv5](https://ftp.ncbi.nlm.nih.gov/blast/db/v5/)). 
-In order to do that, we've implemented a method (`1`) that uses taxids (taxonomic identifiers). 
+In order to do that, we've implemented a method (`1`) that uses taxids (taxonomic groups — species level and higher level taxa). 
 View more about our methods below.
 
-
-Method    |  Description   
+Method    |  Description  
 ----------|--------------------------------------------------------------------
 1         |  Local blast using taxids. Utilizes local databases (`refseq_rna_v5`).
 2         |  Remote blast using an entrez query. Uses entrez species name and query 
 None      |  A single query method not useful for orthology inference
 
-
 #### Our Custom Accession File Format
 
-We use a specifically formatted `accession file` with our headers as `Tier`, `Gene`,
- `Organism` to store blast output and input. This allows for distinguishing genes 
-by families or features. The `Tier` header can be omitted, but the other headers are requirements.
-
+We use a specifically formatted `accession file` with our headers as `Tier`, `Gene`, 
+`Organism` to store blast output and input. This allows for distinguishing genes 
+by families or features. The `Tier` header can be omitted, but the other headers are requirements. 
 The Accession numbers are stored in a `.csv` file.  The following table is an example
 of how we format our blast input file.
 

OrthoEvol/Orthologs/README.md

@@ -1,10 +1,12 @@
 # Orthologs Documentation
+
 This top level module includes submodules such as [Align](https://github.com/datasnakes/OrthoEvolution/blob/master/OrthoEvol/Orthologs/Align/README.md) (for aligning multi fasta files),
 [Phylogenetics](https://github.com/datasnakes/OrthoEvolution/blob/master/OrthoEvol/Orthologs/Phylogenetics/README.md) (for analyzing multiple sequence alignments), [BioSQL]() (for database creation),
 [Blast](https://github.com/datasnakes/OrthoEvolution/tree/master/OrthoEvol/Orthologs/Blast) (includes tools for using NCBI's blastn command line), and [Genbank](https://github.com/datasnakes/OrthoEvolution/blob/master/OrthoEvol/Orthologs/Genbank/README.md).
 (for tools to extract features from genbank files).
 
 ## Usage & Examples
+
 These classes are optimized to be used together (very little work to do that),
 but can also be used as standalone classes/methods.
 

README.rst

@@ -61,13 +61,82 @@ Examples
 ----------------
 Check out this `tutorial <https://github.com/datasnakes/OrthoEvolution/wiki/Tutorial>`__ in our Wiki Docs.
 
+Also, please view `examples <https://github.com/datasnakes/OrthoEvolution/examples>`__ of how to utilize this package to build tools.
+
+
+Running a pre-configured local blast
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. code:: python
 
-    import OrthoEvol
+    from OrthoEvol.Orthologs.Blast import OrthoBlastN
+
+    # Use an existing list of gpcr genes
+    gpcr_blastn = OrthoBlastN(project="orthology-gpcr", method=1,
+                             save_data=True, acc_file="gpcr.csv", 
+                             copy_from_package=True)
+
+    # Run blast
+    gpcr_blastn.run()
+
+
+Simple project creation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. code:: python
+
+    from OrthoEvol.Manager.management import ProjectManagement
+
+    ProjectManagement(repo="test-repo", user=None,
+                      project="test-[roject",
+                      research=None,
+                      research_type='comparative_genetics',
+                      new_repo=False, new_user=False, new_project=True,
+                      new_research=False)
+
+Simple blast database downloading
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. code:: python
+
+    from OrthoEvol.Tools.ftp import NcbiFTPClient
+
+    ncbiftp = NcbiFTPClient(email='[email protected]')
+    ncbiftp.getblastdb(database_name='refseq_rna', v5=True)
+
+Creating projects and databases dynamically 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. code:: python
+
+    from OrthoEvol.Manager.management import ProjectManagement
+    from OrthoEvol.Manager.database_dispatcher import DatabaseDispatcher
+    from OrthoEvol.Manager.config import yml
+    from pkg_resources import resource_filename
+    from pathlib import Path
+    import yaml
+
+    # Set up project management
+    pm_config_file = resource_filename(yml.__name__, "initialize_new.yml")
+    with open(pm_config_file, 'r') as f:
+        pm_config = yaml.load(f)
+    pm = ProjectManagement(**pm_config["Management_config"])
+
+    # Set up database management
+    db_config_file = resource_filename(yml.__name__, "databases.yml")
+    with open(db_config_file, 'r') as f:
+        db_config = yaml.load(f)
+    config = db_config.update(pm_config)
+
+    # Generate main config file for this job
+    config_file = pm.user_log / Path("upload_config.yml")
+    with open(str(config_file), 'w') as cf:
+        yaml.dump(config, cf, default_flow_style=False)
+
+    # Set up database dispatcher and dispatch the functions
+    dd = DatabaseDispatcher(config_file, pm)
+    dd.dispatch(dd.strategies, dd.dispatcher, dd.configuration)
+
 
 Tests
 ----------------
-To run tests, type ``nosetests Tests/`` in the OrthoEvolution directory.
+To run tests, type ``nosetests tests/`` in the OrthoEvolution directory.
 
 Contributors
 ----------------