Added more comments and author / mail description

bin/3.1_create_gtf/Modules/CrossMapper.py

@@ -20,6 +20,7 @@ def __init__(self, org, wd, out, is_dir):
             self.infile = os.path.join(wd+"/data/temp/"+org+".gtf")
         self.outfile = os.path.join(out+"/" + org + "_mapped.gtf")
         self.chainfile = self.get_chain_file(org, wd, is_dir)
+
         # Execute Crossmapper for gff/gtf files
         (mapTree, targetChromSizes, sourceChromSizes) = CrossMap.read_chain_file(self.chainfile)
         CrossMap.crossmap_gff_file(mapTree, self.infile, self.outfile)

bin/3.1_create_gtf/Modules/SaveResults.py

@@ -5,20 +5,35 @@ class ResultSaver:
 
     """
 
-    class to save the results. Path is dependent on the data_dir, tissuetype and mapped = True or False.
+    Class to save the results. Path is dependent on the data_dir, tissuetype and mapped = True or False.
     The output is saved to the temp directory in the data folder if crossmapping is necessary.
 
+    @author: Sebastian Beyvers
+    @contact: sebastian.beyvers@med.uni-giessen.de
+
+
     """
 
     def __init__(self, results, organism, wd,  mapped, is_data_dir, tissue, out):
 
+        # Constructor and main method for result-saving
+        # input_parameter: results     = finished list of gtf-entries
+        #                  organism    = input_organism
+        #                  wd          = working directory
+        #                  mapped      = boolean if crossmapping is necessary
+        #                  is_data_dir = boolean if wd is a data_dir (true) or not (false)
+        #                  is_data_dir = boolean if wd is a data_dir (true) or not (false)
+
+
+        # TODO: DATADIR !!
+
         print("Save results to File !")
         self.path = ""
         if mapped:
             if is_data_dir:
                 self.path = os.path.join(wd + "/temp/" + organism + ".gtf")
             else:
-                self.path = os.path.join( wd + "/data/temp/" + organism + ".gtf" )
+                self.path = os.path.join(wd + "/data/temp/" + organism + ".gtf" )
         elif tissue:
             self.path = os.path.join(out+"/"+organism+"_filtered.gtf")
         else:

bin/3.1_create_gtf/Modules/Uniquifier.py

@@ -1,23 +1,38 @@
 class UniqueFilter:
-
     """
 
     Class to get unique GTF-results, filtered by specified cell-/tissuetypes
 
+    @author: Sebastian Beyvers
+    @contact: sebastian.beyvers@med.uni-giessen.de
+
     """
 
     def __init__(self, ense, ucsc, org_filter=None):
+
+        # Constructor
+        # input_parameter: ense = list of gtf-formatted entries from Ensembl data
+        #                  ucsc = list of gtf-formatted entries from UCSC data
+        #                  org_filter = filter for specific celltype
+
         self.results = self.get_filtered_results(org_filter, ense, ucsc)
 
     def get_results(self):
+
+        # Getter method for results variable
+
         return self.results
 
     def get_filtered_results(self, org_filter, ense, ucsc):
 
-        # Apply Filter
+        # Method to concat ucsc and ensemble dataset without duplicates and filter by activitylist
+        # input_parameter: ense = list of gtf-formatted entries from Ensembl data
+        #                  ucsc = list of gtf-formatted entries from UCSC data
+        #                  org_filter = filter for specific celltype
+        # return_value: List of unique (filtered) results.
 
-        unfiltered_results = self.concat_without_duplicates(ense, ucsc)
-        if org_filter:
+        unfiltered_results = self.concat_without_duplicates(ense, ucsc)  # First: Concat ucsc and ensembl data
+        if org_filter:                                                   # Second: apply filter if specified
             filterstrings = [x+">ACTIVE" for x in org_filter]
             return_list = []
             for element in unfiltered_results:
@@ -32,6 +47,8 @@ def get_filtered_results(self, org_filter, ense, ucsc):
     def concat_without_duplicates(ense, ucsc):
 
         # Concat UCSC and Ensembl data without duplicates
+        # input_parameter: ense = ensembl-gtf-data and ucsc = ucsc-gtf-data
+        # return_value: concatinated list of gtf-entries without duplicates
 
         results = ense+ucsc
         for ens in ense:

bin/3.1_create_gtf/RegGTFExtractor.py

@@ -1,7 +1,7 @@
 """
 
 RegGTFExtractor.py extracts regulatory-data from Ensembl and UCSC databases
-and converts output to GTF-formatted file.
+and converts the output to a GTF-formatted file.
 
 @author: Sebastian Beyvers
 @contact: sebastian.beyvers@med.uni-giessen.de
@@ -21,6 +21,8 @@
 def check_for_local_folder(wd):
 
     # Check if local folder exists and create if missing when no data_dir is specified
+    # input_parameter: wd = working directory
+    # return_value: None
 
     if not os.path.isdir(os.path.join(wd+"/data/")):
 
@@ -40,6 +42,8 @@ def check_for_local_folder(wd):
 def check_for_data_dir(data_dir):
 
     # Check if local folder exists and create if missing when data_dir as parameter is specified
+    # input_parameter: data_dir = data directory
+    # return_value: None
 
     if not os.path.isdir(os.path.join(data_dir)):
         os.mkdir(os.path.join(data_dir))
@@ -57,6 +61,8 @@ def check_for_data_dir(data_dir):
 def check_filter(tissue_cmd, org, wd):
 
     # Checks if filter-celltype is in Json types for organism
+    # input_parameter: tissue_cmd: Filtered tissuetypes; org = organism; wd = working directory
+    # return_value: boolean if selected filter is in config
 
     path_to_config = os.path.join(wd + "/config/celltypes_" + org + ".json")
     tissues_config = []
@@ -77,6 +83,8 @@ def check_filter(tissue_cmd, org, wd):
 def check_organism(org):
 
     # Checks the organism input and decides if chrossmapping is necessary
+    # input_parameter: org = input organism (parameter)
+    # return_value: tuple with values = (organism_alias (string), boolean if chrossmapping is needed)
 
     if org == "hg38":
         return "homo_sapiens", False
@@ -92,7 +100,8 @@ def check_organism(org):
 
 def main_script(organism, wd, data_dir, out, tissuetype=None):
 
-    # Main function
+    # main function
+    # input_parameter: all parameters from argparse
 
     (org,  x_mappable) = check_organism(organism)
     if not data_dir:
@@ -124,7 +133,7 @@ def main_script(organism, wd, data_dir, out, tissuetype=None):
 
 if __name__ == '__main__':
 
-    # Argumentparser
+    # argument parser
 
     parser = argparse.ArgumentParser(description='GTF-Generator from UCSC Table Browser and Ensembl Regulatory Build' )
     parser.add_argument('organism', help='Source organism [ hg19 | hg38 or mm9 | mm10 ]', action='store', nargs='?', type=str)