Adding text and new functions

pgpipe/bed_utilities.py

@@ -153,8 +153,17 @@
         times.
     **--chrom-file** *<chrom_filename>*
         Argument used to define the filename of a file with the sizes of each
-        chromosome file. Appropriate files may be downloaded from the UCSC Genome
-        Browser.
+        chromosome. Chromosome size files must be tab-delimited as follows:
+
+        .. code-block:: bash
+
+            chr1\t247249719
+            chr2\t242951149
+            ...
+            chrX\t154913754
+            chrY\t57772954
+
+        Appropriate files may be downloaded from the UCSC Genome Browser.
     
     #############################
     Output Command-line Arguments
@@ -276,15 +285,26 @@ def metavar_list (var_list):
     bed_parser = argparse.ArgumentParser()
 
     # Input arguments
-    bed_input = bed_parser.add_mutually_exclusive_group(required = True)
+    bed_input = bed_parser.add_mutually_exclusive_group()
     bed_input.add_argument('--bed', help = 'Defines the filename of the BED file', type = str, action = parser_confirm_file())
     bed_input.add_argument('--beds', help = 'Defines the filenames of the BED files (may be used multiple times)', type = str, nargs = '+', action = parser_confirm_file_list())
     bed_parser.add_argument('--chrom-file', help = 'File of chromosome sizes', type = str, action = parser_confirm_file())
 
     # Utility based arguments
-    utility_list = ['sample', 'subtract', 'extend', 'sort', 'merge', 'complement']
+    utility_list = ['sample', 'subtract', 'extend', 'sort', 'merge', 'complement', 'windows', 'intersect']
     bed_parser.add_argument('--utility', metavar = metavar_list(utility_list), help = 'Specifies the utility to be used', type = str, choices = utility_list, required = True)
 
+    # Intersect-specific arguments
+    intersect_group = bed_parser.add_argument_group('Intersect Utility Arguments')
+    intersect_group.add_argument('--intersect-file', help = 'File to intersect', type = str, action = parser_confirm_file())
+    intersect_group.add_argument('--return_only_intersects', help = 'Only return intersecting intervals', action = 'store_true')
+    intersect_group.add_argument('--sorted-intersect', help = 'Invokes the sorted algorithm. Use to reduce memory usage with a large --intersect-file. Requires both files to be sorted in the same manner', action = 'store_true')
+
+    # Window-specific arguments
+    window_group = bed_parser.add_argument_group('Windows Utility Arguments')
+    window_group.add_argument('--window-size', help = 'Size (in bp) of windows to be created', type = int)
+    window_group.add_argument('--window-step', help = 'Step size (in bp) between new windows. Defaults to the window size', type = int)
+
     # Sample-specific arguments
     sample_group = bed_parser.add_argument_group('Sample Utility Arguments')
     sample_group.add_argument('--sample-size', help="Defines the total sample size", type = int)
@@ -429,6 +449,10 @@ def run (**kwargs):
     # Assign arguments
     bed_args = argparse.Namespace(**kwargs)
 
+    # Confirm an input BED has been given, unless windows are being created
+    if bed_args.utility != 'windows' and (not bed_args.bed and not bed_args.beds):
+        raise Exception('--bed or --beds required')
+
     # Adds the arguments (i.e. parameters) to the log file
     logArgs(bed_args, 'bed_utilities')
 
@@ -491,7 +515,7 @@ def run (**kwargs):
     else:
 
         # Check if the utility requires a chromosome size file
-        if bed_args.utility in ['complement', 'extend']:
+        if bed_args.utility in ['complement', 'extend', 'windows']:
 
             # Check if a chromosome sizes file has been defined
             if not bed_args.chrom_file:
@@ -586,6 +610,43 @@ def run (**kwargs):
             # Assign the --chrom-file argument
             bedtools_arg_list.extend(['-g', bed_args.chrom_file])
 
+        # Check if the create windows utility has been selected
+        elif bed_args.utility == 'windows':
+
+            # Assign the utility
+            bedtools_arg_list.append(f'make{bed_args.utility}')
+
+            # Assign the --chrom-file argument
+            bedtools_arg_list.extend(['-g', bed_args.chrom_file])
+
+            # Check if --window-size has been specified 
+            if bed_args.window_size:
+                bedtools_arg_list.extend(['-w', bed_args.window_size])
+
+            # Check if --window-step has been specified 
+            if bed_args.window_step:
+                bedtools_arg_list.extend(['-s', bed_args.window_step])
+
+        # Check if the create intersect utility has been selected
+        elif bed_args.utility == 'intersect':
+
+            # Assign the utility
+            bedtools_arg_list.append(bed_args.utility)
+
+            # Assign the input arguments
+            bedtools_arg_list.extend(['-a', bed_args.bed])
+
+            # Assign the --chrom-file argument
+            bedtools_arg_list.extend(['-b', bed_args.intersect_file])
+
+            # Check if --return-only-intersect has not been specified 
+            if not bed_args.return_only_intersects:
+                bedtools_arg_list.append('-u')
+
+            # Check if --sorted-intersect has not been specified
+            if bed_args.sorted_intersect:
+                bedtools_arg_list.append('-sorted')
+
         # Catch unknown utilities    
         else:
             raise Exception('%s is an unknown utility. Please check input' % bed_args.utility)