ex-269 (jebene/dkriti) began drafting architecture doc -- edited rst and

created abstract methods file

doc/architecture.rst

@@ -0,0 +1,53 @@
+Architectural Overview
+======================
+This overview is intended for contributers.
+
+Coding Standards & Guidelines
+-----------------------------
+ - Uses pylint to format the code.
+ - Uses '_' to separate the words both in variable and method names.
+ - Uses caps to separate the words in the class names.
+ - Uses absolute imports.
+ - Supports Python 2.7 and 3.x.
+
+Commands
+--------
+Jacquard is a suite of Python command line tools. Each tool is contained in a
+module of the same name and called in the jacquard module. Only jacquard.py
+is aware of all of the possible commands. 
+
+Translate
+^^^^^^^^^
+Translate standardizes VCF files by adding Jacquard-specific format tags.
+
+There are two main functions that Translate implements:
+
+**1. Filter flags are added to anomalous VCF records.**
+   Translate initializes several private classes that label anomalous records
+   as such.
+
+**2. New Jacquard-specific format tags are added to VCF records.**
+   Translate calls out to the variant_caller_factory.py, which then adds new 
+   format tag values for each relevant variant caller. Only
+   variant_caller_factory.py is aware of all of the possible variant callers.
+
+
+Merge
+^^^^^
+
+
+
+Summarize
+^^^^^^^^^
+
+Expand
+^^^^^^
+
+Transforms and Tags
+-------------------
+
+Utils
+-----
+
+Test Conventions
+----------------

doc/index.rst

@@ -19,9 +19,13 @@ Contents:
    Merge <merge>
    Summarize <summarize>
    Expand <expand>
+
    FAQ <faq>
+
+   Architectural Overview <architecture>
    Changelog <include_changelog>
    Future Directions <include_todo>
+
    License <license>
 
 

doc/new_tag.py

@@ -0,0 +1,114 @@
+#pylint: disable=pointless-string-statement
+import abc
+
+
+"""Abstract class outlining requirements for adding a new tag to Jacquard"""
+class NewTag(object):
+    #pylint:disable=too-few-public-methods,abstract-class-not-used
+    __metaclass__ = abc.ABCMeta
+
+    @abc.abstractmethod
+    def add_tag_values(self, vcf_record):
+        """Adds format tag and sample values to a VCF record"""
+
+
+
+"""Abstract class outlining requirements for adding a new variant caller to
+   Jacquard."""
+class NewVariantCaller(object):
+    #pylint:disable=too-few-public-methods,abstract-class-not-used
+    __metaclass__ = abc.ABCMeta
+
+    @abc.abstractmethod
+    def claim(self,file_readers):
+        """Recognizes and claims MuTect VCFs form the set of all input VCFs.
+
+        Each defined caller has a chance to evaluate and claim all the incoming
+        files as something that it can process.
+
+        Args:
+            file_readers: the collection of currently unclaimed files
+
+        Returns:
+            A tuple of unclaimed readers and NewVariantCallerReaders.
+        """
+
+
+
+"""Abstract class outlining requirements for adding a new variant
+  caller-specific VcfReader object to Jacquard."""
+class _NewVcfReader(object):
+    #pylint:disable=abstract-class-not-used
+    __metaclass__ = abc.ABCMeta
+
+    @abc.abstractmethod
+    @property
+    def caller_name(self):
+        """returns the caller name"""
+
+    @abc.abstractmethod
+    @property
+    def file_name(self):
+        """returns the file name"""
+
+    @abc.abstractmethod
+    def open(self):
+        """opens the vcf reader"""
+
+    @abc.abstractmethod
+    def close(self):
+        """closes the vcf reader"""
+
+    @abc.abstractmethod
+    @staticmethod
+    def expected_file_format():
+        """returns a list of file groupings (eg ['snp', 'indel']) to be used
+        to later validate that the files are paired together correctly"""
+
+    @abc.abstractmethod
+    @property
+    def metaheaders(self):
+        """adds and returns new metaheaders"""
+
+    @abc.abstractmethod
+    @property
+    def column_header(self):
+        """returns column header"""
+
+    @abc.abstractmethod
+    def tagged_vcf_records(self):
+        """yields tagged vcf_records"""
+
+    @abc.abstractmethod
+    def vcf_records(self):
+        """yields vcf_records"""
+
+
+
+"""Abstract methods outlining requirements for adding a new command to
+   Jacquard."""
+#pylint: disable=unused-argument
+@abc.abstractmethod
+def validate_args(args):
+    """validates command-line arguments"""
+
+@abc.abstractmethod
+def get_required_input_output_types():
+    """Returns a tuple of input and output types.
+
+    Possible values are:
+         'file'
+         'directory'
+    """
+
+@abc.abstractmethod
+def report_prediction(args):
+    """returns a list of output file names be be created"""
+
+@abc.abstractmethod
+def add_subparser(subparser):
+    """uses argparse to add a sub-parser"""
+
+@abc.abstractmethod
+def execute(args, execution_context):
+    """executes private methods"""