--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beagle.py	Mon Oct 15 18:15:47 2018 -0400
@@ -0,0 +1,163 @@
+import os
+import sys
+import subprocess
+import shutil
+import argparse
+import glob
+import logging
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.pardir, 'jared')))
+
+from vcf_reader_func import checkFormat
+from logging_module import initLogger, logArgs
+from vcftools import bgzip_decompress_vcfgz
+from bcftools import convert_to_bcf, check_for_index, create_index
+
+def delete_beagle_log (output_prefix):
+    '''
+        Delete beagle log file
+
+        This function is used to delete beagle's log file if an error is
+        encountered. A warning is produced if the log file cannot be found.
+
+        Parameters
+        ----------
+        output_prefix : str
+            Output file prefix
+    '''
+
+    # Check that log file exists, if not return warning
+    if not os.path.isfile(output_prefix + '.log'):
+        logging.warning('beagle log file %s.log does not exist' % output_prefix)
+    else:
+        os.remove(output_prefix + '.log')
+
+def check_beagle_for_errors (beagle_stderr, output_prefix):
+    '''
+        Checks the beagle stdout for errors
+
+        Parameters
+        ----------
+        beagle_stderr : str
+            beagle stderr
+        output_prefix : str
+            Output file prefix
+
+        Raises
+        ------
+        Exception
+            If beagle stdout returns an error
+    '''
+
+    # Check if beagle completed without an error
+    if not beagle_stderr.strip():
+        pass
+
+    # Print missing data message if that is likely
+    elif 'ERROR: genotype is missing allele separator:' in str(beagle_stderr):
+        # Delete the beagle log file
+        delete_beagle_log(output_prefix)
+
+        # Store reported error
+        error_reported = 'ERROR: genotype is missing allele separator'
+        # Store message for user about error
+        user_message = 'Please confirm the input has no missing data.'
+        # Report on the error
+        raise Exception(error_reported + '\n' + user_message)
+
+    # Print output for beagle if error is detected
+    elif 'ERROR:' in str(beagle_stderr):
+        # Delete the beagle log file
+        delete_beagle_log(output_prefix)
+
+        # Splits log into list of lines
+        beagle_stderr_lines = beagle_stderr.splitlines()
+        # Prints the error(s)
+        raise Exception('\n'.join((output_line for output_line in beagle_stderr_lines if output_line.startswith('ERROR:'))))
+
+    # Print output if not completed and no error found. Unlikely to be used, but included.
+    else:
+        # Delete the beagle log file
+        delete_beagle_log(output_prefix)
+
+        raise Exception(beagle_stderr)
+
+
+def standard_beagle_call (beagle_path, beagle_call_args, output_prefix):
+    '''
+        Calls beagle using subprocess
+
+        This function is used to call beagle under standard conditions. The
+        functions then passes the stderr to check_beagle_for_errors to check
+        for errors.
+
+        Parameters
+        ----------
+        beagle_path : str
+            Path to beagle.jar
+        beagle_call_args : list
+            Argument list for beagle
+        output_prefix : str
+            Output file prefix
+    '''
+
+    # Assign location of beagle jar file
+    beagle_jar = os.path.join(beagle_path, 'beagle.jar')
+
+    # Check that beagle.jar exists
+    if not os.path.isfile(beagle_jar):
+        raise IOError('beagle.jar not found. Path specified: %s' % beagle_path)
+
+    logging.info('beagle phasing parameters assigned')
+
+    # Phasing subprocess call
+    phase_call = subprocess.Popen(['java', '-jar', beagle_jar] + beagle_call_args, stdout = subprocess.PIPE, stderr = subprocess.PIPE)
+    phase_stdout, phase_stderr = phase_call.communicate()
+
+    # Check if code is running in python 3
+    if sys.version_info[0] == 3:
+        # Convert bytes to string
+        phase_stderr = phase_stderr.decode()
+
+    # Check beagle call for errors
+    check_beagle_for_errors(phase_stderr, output_prefix)
+
+    logging.info('beagle phasing complete')
+
+def call_beagle (beagle_path, beagle_call_args, output_prefix, output_format):
+    '''
+        Automates beagle calls
+
+        This function passes the argument list to standard_beagle_call. Once the
+        beagle call has finished, the function will automatically convert the
+        bgzip compressed output of beagle to BCF and VCF, if either format is
+        specified.
+
+        Parameters
+        ----------
+        beagle_path : str
+            Path to beagle.jar
+        beagle_call_args : list
+            Argument list for beagle
+        output_prefix : str
+            Output file prefix
+        output_format : str
+            Output file format
+    '''
+    print beagle_call_args
+    # Standard call to beagle
+    standard_beagle_call(beagle_path, beagle_call_args, output_prefix)
+
+    # Decompress if a VCF files is requested
+    if output_format == 'vcf':
+        bgzip_decompress_vcfgz(output_prefix + '.vcf.gz')
+
+    # Convert to BCF if requested
+    elif output_format == 'bcf':
+
+        # Check if there is an index file
+        if check_for_index(output_prefix + '.vcf.gz') == False:
+            # Create an index if not found
+            create_index(output_prefix + '.vcf.gz')
+        # Convert vcf.gz to bcf
+        convert_to_bcf(output_prefix + '.vcf.gz', output_prefix)