Minor fixes to the genome class

Missed some stuff before merging. Oops.

chipathlon/genome.py

@@ -36,14 +36,6 @@ class Genome(object):
             self.chrom_sizes
         )
 
-    def _load_prefixes(self):
-        self.file_prefix = "genome_%s_%s" % (self.assembly, self.tool)
-        self.add_file_prefix = self.file_prefix if self.tool == "bowtie2" else self.file_prefix + os.path.splitext(self.base_file)[1]
-        bowtie2_path_prefix, base_ext = os.path.splitext(self.base_file)
-        self.base_ext = base_ext
-        self.path_prefix = bowtie2_path_prefix if self.tool == "bowtie2" else self.base_file
-        return
-
     def is_valid(self):
         """
         Checks if the run is valid.
@@ -62,10 +54,28 @@ class Genome(object):
     def get_chrom_sizes(self):
         return self.files.get("chrom_sizes")
 
-    def get_additional(self, gen_file_type):
-        return self.files.get(gen_file_type)
+    def get_additional_files(self):
+        return self.files.get("additional_files")
+
+    def get_chr_fasta_files(self):
+        return self.files.get("chr_fasta")
+
+    def _load_prefixes(self):
+        self.file_prefix = "genome_%s_%s" % (self.assembly, self.tool)
+        self.add_file_prefix = self.file_prefix if self.tool == "bowtie2" else self.file_prefix + os.path.splitext(self.base_file)[1]
+        bowtie2_path_prefix, base_ext = os.path.splitext(self.base_file)
+        self.base_ext = base_ext
+        self.path_prefix = bowtie2_path_prefix if self.tool == "bowtie2" else self.base_file
+        return
 
     def _add_file(self, name, path, gen_file_type="base_file"):
+        """
+        Adds a file to the internal files list.  Files are indexed
+        by type.  There should only be a single base_file / chrom.sizes
+        file, however there can and should be multiple additional genomic
+        files and individual chromsome fasta files.  These additional inputs
+        will be maintained in a list.
+        """
         f = File(name)
         f.addPFN(PFN(path, "local"))
         if gen_file_type == "base_file" or gen_file_type == "chrom.sizes":
@@ -99,33 +109,18 @@ class Genome(object):
         return
 
     def _load_files(self):
+        # Load in the base file / chromsome sizes file
         self._add_file("%s.%s" % (self.file_prefix, self.base_ext), self.base_file, "base_file")
         self._add_file("%s.chrom.sizes" % (self.file_prefix,), self.chrom_sizes, "chrom.sizes")
+        # Load each additional file
         for ext in chipathlon.conf.genomes[self.tool]["additional_files"]:
             name = "%s.%s" % (self.add_file_prefix, ext)
             path = "%s.%s" % (self.path_prefix, ext)
             self._add_file(name, path, "additional_files")
+        # Load each individual chromsome fasta file
         base_dir = os.path.dirname(os.path.dirname(self.chrom_sizes + "/"))
         for root, dirs, files in os.walk(base_dir):
             for f in files:
                 if f.startswith("chr"):
                     self._add_file("%s_%s" % (self.add_file_prefix, f), root + "/" + f, "chr_fasta")
         return
-
-    def _valid_genome(self, run):
-        """
-        :param run: The run to check.
-        :type run: dict
-
-        Check that the provided run has a genome that exists.
-        """
-        valid = False
-        if run["genome"] in self.genomes:
-            if run["align"] in self.genomes[run["genome"]]:
-                valid = True
-                msg = "Genome is valid."
-            else:
-                msg = "Alignment tool '%s' not defined for genome '%s'." % (run["align"], run["genome"])
-        else:
-            msg = "Run genome '%s' not defined in genome data." % (run["genome"],)
-        return (valid, msg)