diff shapeit.py @ 0:3830d29fca6a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shapeit.py	Mon Oct 15 18:15:47 2018 -0400
@@ -0,0 +1,160 @@
+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 plink import convert_haps_to_vcf
+#from vcftools import bgzip_decompress_vcfgz
+#from bcftools import convert_to_bcf, check_for_index, create_index
+
+def check_shapeit_for_errors (shapeit_stdout, output_prefix):
+    '''
+        Checks the shapeit stdout for errors
+
+        Parameters
+        ----------
+        shapeit_stdout : str
+            shapeit stdout
+        output_prefix : str
+            Output filename prefix
+
+        Raises
+        ------
+        Exception
+            If shapeit stdout returns an error
+    '''
+
+    # Returns True if the job completed without error
+    if 'Running time:' in str(shapeit_stdout):
+        pass
+
+    # Print output if not completed and no error found. Unlikely to be used, but included.
+    else:
+        # Remove intermediate files before reporting the error
+        remove_intermediate_files(output_prefix, error_intermediates = True)
+        raise Exception(str(shapeit_stdout))
+
+def remove_intermediate_files (output_prefix, error_intermediates = False):
+    '''
+        Removes shapeit intermediate files
+
+        This function is used to remove the various intermediate files created
+        by shapeit. The exact intermediate files to be removed are defined by
+        the error-state of shapeit. The function will also return warnings if
+        the intermediate files were not found.
+
+        Parameters
+        ----------
+        output_prefix : str
+            Output filename prefix
+        error_intermediates : bool, optional
+            Defines if shapeit encountered an error
+
+    '''
+    if error_intermediates:
+
+        # Check that the log file was created, give a warning otherwise
+        if not os.path.isfile(output_prefix + '.phase.log'):
+            logging.warning('shapeit intermediate file %s.phase.log does not exist' % output_prefix)
+        else:
+            # Remove shapeit log file
+            os.remove(output_prefix + '.phase.log')
+
+    else:
+
+        # Check that the phase.ind.mm file was created, give a warning otherwise
+        if not os.path.isfile(output_prefix + '.phase.ind.mm'):
+            logging.warning('shapeit intermediate file %s.phase.ind.mm does not exist' % output_prefix)
+        else:
+            # Remove shapeit phase.ind.mm file
+            os.remove(output_prefix + '.phase.ind.mm')
+
+        # Check that the phase.snp.mm file was created, give a warning otherwise
+        if not os.path.isfile(output_prefix + '.phase.snp.mm'):
+            logging.warning('shapeit intermediate file %s.phase.snp.mm does not exist' % output_prefix)
+        else:
+            # Remove shapeit phase.snp.mm file
+            os.remove(output_prefix + '.phase.snp.mm')
+
+    # Check that the haps file was created, give a warning otherwise
+    if not os.path.isfile(output_prefix + '.haps'):
+        logging.warning('shapeit intermediate file %s.haps does not exist' % output_prefix)
+    else:
+        # Remove shapeit haps file
+        os.remove(output_prefix + '.haps')
+
+    # Check that the sample file was created, give a warning otherwise
+    if not os.path.isfile(output_prefix + '.sample'):
+        logging.warning('shapeit intermediate file %s.sample does not exist' % output_prefix)
+    else:
+        # Remove shapeit sample file
+        os.remove(output_prefix + '.sample')
+
+    logging.info('shapeit-related files removed')
+
+def standard_shapeit_call (shapeit_call_args, output_prefix):
+    '''
+        Calls shapeit using subprocess
+
+        This function is used to call shapeit and passes the resulting stdout
+        to check_shapeit_for_errors to check for errors. The function also
+        passes output_prefix to check_shapeit_for_errors to delete shapeit
+        intermediate files if shapeit results in an error.
+
+        Parameters
+        ----------
+        shapeit_call_args : list
+            Argument list for shapeit
+        output_prefix : str
+            Output filename prefix
+
+    '''
+
+    logging.info('shapeit phasing parameters assigned')
+
+    # Phasing subprocess call
+    phase_call = subprocess.Popen(['shapeit'] + shapeit_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_stdout = phase_stdout.decode()
+
+    # Check shapeit call for errors
+    check_shapeit_for_errors(phase_stdout, output_prefix)
+
+    logging.info('shapeit phasing complete (HAPS format)')
+
+def call_shapeit (shapeit_call_args, output_prefix, output_format):
+    '''
+        Calls shapeit and automates file conversions
+
+        The function is used to call shapeit and also automates conversion to
+        VCF, VCF.GZ, and BCF using plink2
+
+        Parameters
+        ----------
+        shapeit_call_args : list
+            Argument list for shapeit
+        output_prefix : str
+            Output filename prefix
+        output_format : str
+            Output file format
+
+    '''
+
+    # Standard call to beagle
+    standard_shapeit_call(shapeit_call_args, output_prefix)
+
+    # Convert haps-format to vcf
+    convert_haps_to_vcf(output_prefix, output_format)
+
+    logging.info('HAPS conversion to VCF complete')