Updated autodoc and rst for genome.

chipathlon/genome.py

@@ -3,18 +3,22 @@ import chipathlon.conf
 from Pegasus.DAX3 import File, PFN
 
 class Genome(object):
+    """
+    :param assembly: Version of genome used for building i.e. hg19, grch38p6, mm9
+    :type assembly: string
+    :param tool: Tool used to create the genome.
+    :type tool: string
+    :param base_file: Main genome file probably a .fna or .fa file.
+    :type base_file: string
+    :param chrom_sizes: Chromsome sizes file.
+    :type chrom_sizes: string
+
+    The genome handles loading and validating genome files on the disk.
+    It servers as a helper class to make managing genome input files
+    much easier.
+    """
 
     def __init__(self, assembly, tool, base_file, chrom_sizes):
-        """
-        :param assembly: Version of genome used for building i.e. hg19, grch38p6, mm9
-        :type assembly: string
-        :param tool: Tool used to create the genome.
-        :type tool: string
-        :param base_file: Main genome file probably a .fna or .fa file.
-        :type base_file: string
-        :param chrom_sizes: Chromsome sizes file.
-        :type chrom_sizes: string
-        """
         self.assembly = assembly
         self.tool = tool
         self.base_file = base_file
@@ -38,7 +42,7 @@ class Genome(object):
 
     def is_valid(self):
         """
-        Checks if the run is valid.
+        Checks if the genome is valid.
         """
         return len(self.errors) == 0
 
@@ -49,18 +53,39 @@ class Genome(object):
         return "\n".join(self.errors)
 
     def get_base_file(self):
+        """
+        :returns: The full name of the base file.
+        """
         return self.files.get("base_file")
 
     def get_chrom_sizes(self):
+        """
+        :returns: The full name of the chromosome sizes file.
+        """
         return self.files.get("chrom.sizes")
 
     def get_additional_files(self):
+        """
+        :returns: A list of all additional genome indices.
+
+        For bwa returns the file names of the .amb, .ann, .bwt, .pac, and .sa
+        files.  For bowtie2 returns the file names of the .1.bt2, .2.bt2,
+        .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2 files.
+        """
         return self.files.get("additional_files")
 
     def get_chr_fasta_files(self):
+        """
+        :returns: A list of all individual chromsome fasta files (if they exist)
+        """
         return self.files.get("chr_fasta")
 
     def get_all_files(self):
+        """
+        :returns: A list of all files:  The base file, the chromsome sizes
+        file, all additional genome indices, and all individual chromosme
+        fasta files.
+        """
         return [self.get_base_file(), self.get_chrom_sizes()] + self.get_additional_files() + self.get_chr_fasta_files()
 
     def _load_prefixes(self):

doc/source/genome.rst

 Genome
 ==============
 
+Genome Class
+^^^^^^^^^^^^^
+
 .. autoclass:: chipathlon.genome.Genome
     :members: