changeset 4:901857c9b24f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plink.py	Wed Oct 17 17:30:37 2018 -0400
@@ -0,0 +1,214 @@
+import os
+import sys
+import subprocess
+import shutil
+import argparse
+import glob
+import copy
+import logging
+import re
+
+# Call PPP-based scripts
+sys.path.insert(0, os.path.abspath(os.path.join(os.pardir,'jared')))
+
+from bcftools import convert_to_bcf
+from logging_module import initLogger, logArgs
+
+def assign_delim_from_ids (filename, id_column = 0, default_delim = '_'):
+
+    delim_symbols = ['-', '|', '/', '@', '&', '*', '^', '%', '$']
+
+    symbols_present = []
+
+    with open(filename, 'rU') as sample_file:
+        for line_pos, sample_line in enumerate(sample_file):
+            if line_pos > 1:
+                # Stores the current sample ID
+                sample_id = sample_line.strip().split()[id_column]
+                # Symbols found in the sample ID
+                id_symbols = re.sub(r'[a-zA-Z0-9]','', sample_id)
+                # Iterate the symbols from the ID
+                for id_symbol in iter(id_symbols):
+                    # Check if that symbol has been stored
+                    if id_symbol not in symbols_present:
+                        # Store symbols
+                        symbols_present.append(id_symbol)
+
+    if default_delim not in symbols_present:
+        return default_delim
+    else:
+        for delim_symbol in delim_symbols:
+            if delim_symbol not in symbols_present:
+                return delim_symbol
+
+    raise IOError('Cannot assign plink delimiter')
+
+def convert_haps_to_vcf (haps_prefix, output_format, output_prefix = ''):
+
+    # Check that input files included a haps file
+    if not os.path.isfile(haps_prefix + '.haps'):
+        # Return error message if no haps input was found
+        raise IOError('Unable to assign haps file. Please confirm the prefix and/or command is specified correctly')
+
+    # Check that input files included a sample file
+    if not os.path.isfile(haps_prefix + '.sample'):
+        # Return error message if no sample input was found
+        raise IOError('Unable to assign sample file. Please confirm the prefix and/or command is specified correctly')
+
+    haps_input_args = ['--haps', haps_prefix + '.haps', 'ref-first', '--sample', haps_prefix + '.sample']
+
+    # If no output_prefix is assigned, use haps_prefix
+    if not output_prefix:
+        output_prefix = haps_prefix
+
+    plink_delim = assign_delim_from_ids(haps_prefix + '.sample')
+
+    if output_format == 'vcf':
+        haps_output_args = ['--recode', 'vcf-iid', 'id-delim=' + plink_delim, '--out', output_prefix]
+
+    elif output_format == 'vcf.gz':
+        haps_output_args = ['--recode', 'vcf-iid', 'bgz', 'id-delim=' + plink_delim, '--out', output_prefix]
+
+    elif output_format == 'bcf':
+        haps_output_args = ['--recode', 'vcf-iid', 'bgz', 'id-delim=' + plink_delim, '--out', output_prefix]
+
+    else:
+        raise IOError('Unknown file format. This error should NOT show up')
+
+    # Call plink2
+    standard_plink2_call(haps_input_args + haps_output_args)
+
+    # Convert VCFGZ to BCF, as PLINK cannot directly create a BCF
+    if output_format == 'bcf':
+        # Convert to BCF
+        convert_to_bcf(output_prefix + '.vcf.gz', output_prefix)
+
+def check_plink_for_errors (plink_stderr):
+    '''
+        Checks the plink stderr for errors
+
+        Parameters
+        ----------
+        plink_stderr : str
+            plink stderr
+
+        Raises
+        ------
+        IOError
+            If plink stderr returns an error
+    '''
+
+    # Print output if error found. Build up as errors are discovered
+    if plink_stderr:
+        raise Exception(plink_stderr)
+
+def standard_plink2_call (plink2_call_args):
+    '''
+        Standard call of plink2
+
+        The function calls plink2. Returns the stderr of plink to create a log
+        file of the call.
+
+        Parameters
+        ----------
+        plink2_call_args : list
+            plink2 arguments
+
+        Raises
+        ------
+        Exception
+            If plink2 stderr returns an error
+    '''
+
+
+    # plink subprocess call
+    plink2_call = subprocess.Popen(['plink2'] + list(map(str, plink2_call_args)), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+    # Wait for plink to finish
+    plink2_out, plink2_err = plink2_call.communicate()
+
+    # Check if code is running in python 3
+    if sys.version_info[0] == 3:
+        # Convert bytes to string
+        plink2_out = plink2_out.decode()
+        plink2_err = plink2_err.decode()
+
+    logging.info('plink2 call complete')
+
+    # Check that the log file was created correctly
+    check_plink_for_errors(plink2_err)
+
+def standard_plink_call (plink_call_args):
+    '''
+        Standard call of plink
+
+        The function calls plink. Returns the stderr of plink to create a log
+        file of the call.
+
+        Parameters
+        ----------
+        plink_call_args : list
+            plink arguments
+
+        Raises
+        ------
+        Exception
+            If plink stderr returns an error
+    '''
+
+    # plink subprocess call
+    plink_call = subprocess.Popen(['plink'] + list(map(str, plink_call_args)), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+    # Wait for plink to finish
+    plink_out, plink_err = plink_call.communicate()
+
+    # Check if code is running in python 3
+    if sys.version_info[0] == 3:
+        # Convert bytes to string
+        plink_out = plink_out.decode()
+        plink_err = plink_err.decode()
+
+    logging.info('plink call complete')
+
+    # Check that the log file was created correctly
+    check_plink_for_errors(plink_err)
+
+def call_plink (plink_call_args, output_prefix, output_format):
+    '''
+        Determines which version of plink (plink1.9 vs. plink2a) to call
+
+        The function is required for the plink wrapper to determine the needed
+        plink version and also automates conversion to BCF, which both versions
+        of plink do not support.
+
+        Parameters
+        ----------
+        plink_call_args : list
+            plink arguments
+        output_prefix : str
+            Output prefix for non-plink conversions
+        output_format : str
+            Output format for non-plink conversions
+
+    '''
+
+    # Check if the call requries plink2 to operate. This function should be
+    # removed once plink2 is out of alpha
+    if '--haps' in plink_input_args:
+        # Convert vcf id system for plink 1.9 to plink 2
+        if 'vcf-iid' in plink_call_args:
+            format_index = plink_call_args.index('vcf-iid')
+            plink_call_args[format_index:format_index + 1] = ['vcf', 'id-paste=fid']
+
+        # Call the plink2 subprocess function
+        standard_plink2_call(plink_call_args)
+
+    # Call plink1.9
+    else:
+        # Call the plink subprocess function
+        standard_plink_call(plink_call_args)
+
+    # Convert VCFGZ to BCF, as PLINK cannot directly create a BCF
+    if output_format == 'bcf':
+        # Convert to BCF
+        convert_to_bcf(output_prefix + '.vcf.gz', output_format)