various changes

pgpipe/__init__.py

@@ -17,7 +17,7 @@
 
 # Basic Information
 __title__     = "py-popgen"
-__version__   = '0.1.7'
+__version__   = '0.1.10'
 __summary__   = "Software platform for facilitating population genomic analyses"
 __url__       = "https://ppp.csusm.edu/"
 __license__   = "MIT"

pgpipe/admixture.py

@@ -110,9 +110,9 @@
 
 from pgpipe.logging_module import initLogger, logArgs
 from pgpipe.plink import confirm_ped_prefix, confirm_bed_prefix, confirm_ped_files, confirm_bed_files
-from pgpipe.misc import confirm_executable
+from pgpipe.misc import confirm_executable, argprase_kwargs
 
-def admix_parser(passed_arguments):
+def admix_parser(passed_arguments = []):
     '''admix Argument Parser - Assigns arguments from command line'''
 
     def parser_confirm_file ():
@@ -171,15 +171,18 @@ def metavar_list (var_list):
 
 
     if passed_arguments:
-        return admix_parser.parse_args(passed_arguments)
+        return vars(admix_parser.parse_args(passed_arguments))
     else:
-        return admix_parser.parse_args()
+        return vars(admix_parser.parse_args())
 
+def run(**kwargs):
 
-def run(passed_arguments = []):
+    # Update kwargs with defaults
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs, admix_parser)
 
-    # Grab admixture arguments from command line
-    admix_args = admix_parser(passed_arguments)
+    # Assign arguments
+    admix_args = argparse.Namespace(**kwargs)
 
     # Adds the arguments (i.e. parameters) to the log file
     logArgs(admix_args, func_name = 'admixture')    
@@ -277,9 +280,7 @@ def run(passed_arguments = []):
     # Check if the executable was found
     if not admixture_path:
         raise IOError('admixture not found. Please confirm the executable is installed')
-
-    #admixture_path = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),'bin','admixture')
-
+
     # Run 'admixture' executable file with options provided by user
     admixture_call = subprocess.Popen([admixture_path] + list(map(str, admix_call_args)), stdout = subprocess.PIPE, stderr = subprocess.PIPE)
 
@@ -292,4 +293,4 @@ def run(passed_arguments = []):
 
 if __name__ == "__main__":
     initLogger()
-    run()
+    run(**admix_parser())

pgpipe/bed_utilities.py

@@ -6,9 +6,9 @@
     a single BED; v) merge features within one or more BED files; vi) create a BED of 
     complementary features.
 
-    ******************
+    ##################
     Command-line Usage
-    ******************
+    ##################
     The BED utilites function may be called using the following command:
 
     .. code-block:: bash
@@ -20,6 +20,22 @@
     Utilites
     ########
 
+    ***************
+    Windows Utility
+    ***************
+
+    Given a chromosome size file and a window size, the windows utility will generate a 
+    BED file of interval features.
+
+    =============
+    Example usage
+    =============
+    Return a BED with interval features that do not extend outside the chromosomes:
+
+    .. code-block:: bash
+        
+        bed_utilities.py --utility windows --chrom-file hg18.chrom.sizes --window-size 1000 --out hg18_windows.bed
+
     **************
     Sample Utility
     **************
@@ -116,6 +132,22 @@
         
         bed_utilities.py --utility complement --bed examples/files/chr1_sites.bed --chrom-file examples/files/chr_sizes.txt
 
+    *****************
+    Intersect Utility
+    *****************
+
+    Given a BED file and an intersect file, return only the interval features within the BED
+    file that overlap with the intersect file. 
+
+    =============
+    Example usage
+    =============
+    Return a BED with only intersecting interval features:
+
+    .. code-block:: bash
+        
+        bed_utilities.py --utility intersect --bed hg18_windows.bed --intersect-file Intersect.vcf.gz --out hg18_intersects.bed
+
     *************
     Merge Utility
     *************
@@ -153,8 +185,20 @@
         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 <http://hgdownload.soe.ucsc.edu/downloads.html>`_. 
+        The supported **ASSEMBLY.chrom.sizes** file for each assembly may be found by 
+        clicking **Genome sequence files and select annotations** (followed by
+        **Standard genome sequence files and select annotations** on select assemblies).
     
     #############################
     Output Command-line Arguments
@@ -176,6 +220,12 @@
         files (merge); create a BED file of complementary features - i.e. features that 
         do not overlap - from a BED file (complement).
 
+    *************************************
+    Window Utility Command-line Arguments
+    *************************************
+    **--window-size** *<window_size_int>*
+        Argument used to define the window/interval size to return.
+
     *************************************
     Sample Utility Command-line Arguments
     *************************************
@@ -219,6 +269,14 @@
         Argument used to define the length of base pairs (bp) to extend downstream of 
         features.
 
+    ****************************************
+    Intersect Utility Command-line Arguments
+    ****************************************
+    **--intersect-file** *<intersect_file_filename>*
+        Argument used to define the BED/VCF/VCF.gz file used to remove features that 
+        do not intersect with the given file's features/variants.
+        removing features/positions.
+
     ************************************
     Merge Utility Command-line Arguments
     ************************************
@@ -276,15 +334,26 @@ 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 +498,10 @@ 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 +564,7 @@ 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 +659,43 @@ 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)

pgpipe/eigenstrat_fstats.py

@@ -185,8 +185,9 @@
 from pgpipe.eigenstrat_wrapper import *
 from pgpipe.model import read_model_file, pops_not_in_model
 from pgpipe.logging_module import initLogger, logArgs
+from pgpipe.misc import argprase_kwargs
 
-def admix_parser (passed_arguments):
+def admix_parser (passed_arguments = []):
     '''admix Argument Parser - Assigns arguments from command line'''
 
     def parser_confirm_file ():
@@ -265,9 +266,9 @@ def metavar_list (var_list):
     admix_parser.add_argument('--admix-o-pop-file', dest = 'o_file', help = 'O populations for admixure analysis', type = str, action = parser_confirm_file())
 
     if passed_arguments:
-        return admix_parser.parse_args(passed_arguments)
+        return vars(admix_parser.parse_args(passed_arguments))
     else:
-        return admix_parser.parse_args()
+        return vars(admix_parser.parse_args())
 
 def read_admix_pops_file (pop_filename):
 
@@ -286,10 +287,14 @@ def read_admix_pops_file (pop_filename):
     # Return the admix pops
     return admix_pops
 
-def run(passed_arguments = []):
+def run(**kwargs):
 
-    # Grab admixtools arguments from command line
-    admix_args = admix_parser(passed_arguments)
+    # Update kwargs with defaults
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs, admix_parser)
+
+    # Assign arguments
+    admix_args = argparse.Namespace(**kwargs)
 
     # Adds the arguments (i.e. parameters) to the log file
     logArgs(admix_args, func_name='admixtools')
@@ -555,4 +560,4 @@ def run(passed_arguments = []):
 
 if __name__ == "__main__":
     initLogger()
-    run()
+    run(**admix_parser())

pgpipe/fasta_utilities.py

@@ -7,14 +7,12 @@
 import logging
 import pandas as pd
 
-# Insert Jared's directory path, required for calling Jared's functions. Change when directory structure changes.
-#sys.path.insert(0, os.path.abspath(os.path.join(os.pardir, 'pppipe')))
-
 from pgpipe.logging_module import initLogger, logArgs
 
 from pgpipe.picard import call_picard
+from pgpipe.misc import argprase_kwargs
 
-def fasta_utility_parser(passed_arguments):
+def fasta_utility_parser(passed_arguments = []):
     '''fasta Argument Parser - Assigns arguments from command line'''
 
     def parser_confirm_file ():
@@ -55,11 +53,11 @@ def metavar_list (var_list):
     fasta_parser.add_argument('--picard-path', help = "Defines path to locate picard.jar", type = str)
 
     if passed_arguments:
-        return fasta_parser.parse_args(passed_arguments)
+        return vars(fasta_parser.parse_args(passed_arguments))
     else:
-        return fasta_parser.parse_args()
+        return vars(fasta_parser.parse_args())
 
-def run (passed_arguments = []):
+def run (**kwargs):
     '''
     Liftover for VCF-formatted files
 
@@ -95,8 +93,12 @@ def run (passed_arguments = []):
         Output file already exists
     '''
 
-    # Grab FASTA arguments from command line
-    fasta_args = fasta_utility_parser(passed_arguments)
+    # Update kwargs with defaults
+    if __name__ != "__main__":
+        kwargs = argprase_kwargs(kwargs, fasta_utility_parser)
+
+    # Assign arguments
+    fasta_args = argparse.Namespace(**kwargs)
 
     # Adds the arguments (i.e. parameters) to the log file
     logArgs(fasta_args, func_name = 'fasta_utilities')
@@ -115,5 +117,5 @@ def run (passed_arguments = []):
 
 
 if __name__ == "__main__":
-    #initLogger()
-    run()
+    initLogger()
+    run(**fasta_utility_parser())

pgpipe/model.py

@@ -100,7 +100,7 @@ def create_ind_file (self, file_ext = '', file_path = '', overwrite = False):
         if not overwrite:
             # Check if the file already exists
             if os.path.isfile(ind_filename):
-                raise IOError('Individuals file exists.')
+                raise IOError('Individuals file exists. Use --overwrite to ignore')
 
         # Create the population file
         ind_file = open(ind_filename, 'w')

pgpipe/plink.py

@@ -468,7 +468,7 @@ def check_plink_for_errors (plink_stderr):
 
     # Print warning, if found
     if 'Warning' in plink_stderr:
-        logging.warning(plink_stderr)
+        logging.warning(plink_stderr.replace('\n',' '))
 
     # Print output if error found. Build up as errors are discovered
     elif plink_stderr: