Added and updated docstrings.

OrthoEvol/Orthologs/Blast/base_blastn.py

@@ -68,18 +68,27 @@ def __init__(self, project, method, template=None, save_data=True, quiet=True, *
         self.complete_time_file = self.project + '_TIME.csv'
         self.complete_time_file_path = self.data / Path(self.complete_time_file)
 
-        self.blastn_parameters, self.query_config = self.select_method(method=self.method)
+        self.blastn_parameters, self.query_config = BaseBlastN.select_method(method=self.method)
 
     def _make_blast_dir(self, gene, path):
-        """Create a blast directory for a gene."""
+        """Create a blast directory for a gene.
+
+        :param gene:  A gene that will be run with blastn.
+        :param path:  The path of the gene directory named with the gene name.
+        """
         try:
             Path.mkdir(path, exist_ok=True, parents=True)
             self.blastn_log.debug("Directory created for %s" % gene)
         except FileExistsError:
             self.blastn_log.debug("Directory exists for %s" % gene)
 
     def _create_temp_fasta(self, query, gene, query_config):
-        """Create a temporary fasta file using blastdbcmd."""
+        """Create a temporary fasta file using blastdbcmd.
+
+        :param query: The blast query or reference accession.
+        :param gene: The gene name of the accession.
+        :param query_config: A configuration dict for the blastdbcmd string.
+        """
         try:
             blastdbcmd_query = "blastdbcmd -entry {query} -db {db} -outfmt %f -out {temp fasta}".format(**query_config)
             blastdbcmd_status = run(blastdbcmd_query, stdout=PIPE,
@@ -97,10 +106,11 @@ def _create_temp_fasta(self, query, gene, query_config):
                 with contextlib.suppress(ValueError):
                     self.current_gene_list.remove(gene)
 
-    def select_method(self, method):
+    @staticmethod
+    def select_method(method):
         """Select a method for running blastn.
 
-        :param method: a blast method - 1, 2, 3, or None
+        :param method: The blast method to use. Either 1, 2, or 3.
         """
         # Local blast using seqidlist
         if method == 1:
@@ -140,7 +150,7 @@ def select_method(self, method):
                             'temp fasta': ''}
         else:
             raise ValueError('%s is not a blast method.' % method)
-        return (blastn_parameters, query_config)
+        return blastn_parameters, query_config
 
     def configure(self, query_accessions, query_organism, auto_start=False):
         """This method configures everything for our BLAST workflow.
@@ -227,7 +237,8 @@ def parse_xml(self, xml_path, gene, organism):
                 for hsp in hit.hsps:
                     # Find the highest scoring hit for each gene
                     if hsp.bitscore_raw > maximum:
-                        # If the gene is a predicted non-coding RefSeq gene then go the the next hit
+                        # If the gene is a predicted non-coding RefSeq gene
+                        # then go the the next hit
                         # https://en.wikipedia.org/wiki/RefSeq
                         if "xr" in str(hit.id.lower()):
                             self.blastn_log.info("Encountered a predicted(X*_00000) "

OrthoEvol/Orthologs/Blast/comparative_genetics.py

@@ -55,11 +55,13 @@ def __init__(self, project=None, project_path=os.getcwd(), acc_file=None,
         downstream processing or for basic observation of the data.
 
         :param project:  The name of the project.
-        :param project_path:  The location of the project, which is generally defined by the ProjectManagement configuration.
+        :param project_path:  The location of the project, which is generally
+                            defined by the ProjectManagement configuration.
         :param acc_file:  The name of the accession file.
         :param taxon_file:  A file that contains an ordered list of taxonomy ids.
-        :param pre_blast:  A flag that gives the user access to an API that contains extra information about their genes
-                           using the mygene package.
+        :param pre_blast:  A flag that gives the user access to an API that
+                        contains extra information about their genes using the
+                        mygene package.
         :param post_blast:  A flag that is used to handle a BLAST result file, which returns information about misssing
                             data, duplicates, etc.
         :param hgnc:  A flag used as a placeholder for future work with HGNC files.
@@ -121,7 +123,8 @@ def __init__(self, project=None, project_path=os.getcwd(), acc_file=None,
             self.taxon_path = self.project_index / Path(self.__taxon_filename)
         # Handle the master accession file (could be before or after blast)
         if self.copy_from_package:
-            shutil.copy(pkg_resources.resource_filename(data.__name__, kwargs['MAF']), str(self.project_index))
+            shutil.copy(pkg_resources.resource_filename(data.__name__, kwargs['MAF']),
+                        str(self.project_index))
             self.acc_file = self.MAF = kwargs['MAF']
             self.acc_filename = self.acc_file
         if self.acc_file is not None:
@@ -169,12 +172,14 @@ def __init__(self, project=None, project_path=os.getcwd(), acc_file=None,
             self.building = pd.read_csv(str(self.acc_path), dtype=str)
             del self.building['Tier']
             del self.building[self.species]
-            self.building = self.building.set_index('Gene')  # Object for good user output
+            # Object for good user output
+            self.building = self.building.set_index('Gene')
             self.building_file_path = self.data / Path(self.building_filename)
 
             # Blast time points
+            # Master time file for the blast
             self.building_time_filename = self.building_filename.replace(
-                'building.csv', 'building_time.csv')  # Master time file for the blast
+                'building.csv', 'building_time.csv')
             self.building_time = pd.read_csv(str(self.acc_path), dtype=str)
             del self.building_time['Tier']
             del self.building_time[self.species]
@@ -218,8 +223,8 @@ def __init__(self, project=None, project_path=os.getcwd(), acc_file=None,
             self.gene_dict = self.df.T.to_dict()
             self.get_master_lists(self.__data)  # populates our lists
         else:
-            self.building_filename = str(self.project + 'building.csv')
-            self.building_time_filename = str(self.project + 'building_time.csv')
+            self.building_filename = str(self.project + '_building.csv')
+            self.building_time_filename = str(self.project + '_building_time.csv')
 
 
 # //TODO-ROB Add HGNC python module
@@ -229,9 +234,8 @@ def get_file_list(file):
 
         :param file: Name of csv file.
         """
-
-        data = pd.read_csv(file, header=None)
-        file_list = list(data[0])
+        file_data = pd.read_csv(file, header=None)
+        file_list = list(file_data[0])
         return file_list
 
     def get_master_lists(self, df, csv_file=None):

OrthoEvol/Orthologs/Blast/orthologs_blastn.py

@@ -8,7 +8,7 @@ class OrthoBlastN(BaseBlastN):
     def __init__(self, project="orthology-gpcr", method=3, template=None,
                  save_data=True, acc_file="gpcr.csv", copy_from_package=True,
                  **kwargs):
-        """This class inherits from the CompGenFiles class.
+        """This class inherits from the BaseBlastN class.
 
         This class utilizes it's parent classes to search a standalone
         Blast database for specific orthologs of a gene using a query organism
@@ -21,6 +21,7 @@ def __init__(self, project="orthology-gpcr", method=3, template=None,
         :param template:  The accession file template.
         :param save_data:  A flag for saving the post_blast data to an excel file.
         :param acc_file: The accession file to use. (Default: 'karg.csv')
+        :param copy_from_package: Copy the acc_file from the package. (Default: True)
         :param kwargs:
         """
         # Set values for methods to prevent using a config.
@@ -43,4 +44,5 @@ def __init__(self, project="orthology-gpcr", method=3, template=None,
                          proj_mana=self.proj_mana, **kwargs)
 
     def run(self):
+        """Run the blast using a default configuration."""
         self.configure(self.blast_human, self.species, auto_start=True)