diff bcftools.py @ 0:3830d29fca6a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools.py	Mon Oct 15 18:15:47 2018 -0400
@@ -0,0 +1,131 @@
+import os
+import sys
+import logging
+import subprocess
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.pardir,'jared')))
+
+from vcf_reader_func import checkFormat
+
+def check_bcftools_for_errors (bcftools_stderr):
+    '''
+        Checks the bgzip stderr for errors
+
+        Parameters
+        ----------
+        bcftools_stderr : str
+            bcftools stderr
+
+        Raises
+        ------
+        IOError
+            If bcftools stderr returns an error
+    '''
+
+    # Expand as errors are discovered
+    if bcftools_stderr:
+        logging.error(vcftools_stderr)
+        raise Exception(vcftools_stderr)
+
+def call_bcftools (bcftools_call_args):
+
+    # bcftools subprocess call
+    bcftools_call = subprocess.Popen(['bcftools'] + list(map(str, bcftools_call_args)), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+    # Wait for bcftools to finish
+    bcftools_out, bcftools_err = bcftools_call.communicate()
+
+    check_bcftools_for_errors(bcftools_err)
+
+    logging.info('bcftools call complete')
+
+def check_for_index (filename):
+
+    # Assign the file format
+    file_format = checkFormat(filename)
+
+    # Check if the file to be indexed is a vcf.gz
+    if file_format == 'bgzip':
+        # Check if the index (.tbi) exists
+        if os.path.isfile(filename + '.tbi'):
+            return True
+
+    # Check if the file to be indexed is a bcf
+    elif file_format == 'bcf':
+        # Check if the index (.csi) exists
+        if os.path.isfile(filename + '.csi'):
+            return True
+
+    # Return false if no index is found
+    return False
+
+def create_index (filename):
+
+    # Assign the file format
+    file_format = checkFormat(filename)
+
+    # Check if the file to be indexed is a vcf.gz
+    if file_format == 'bgzip':
+        # Create a index (.tbi)
+        call_bcftools(['index', '-t', filename])
+
+    # Check if the file to be indexed is a bcf
+    elif file_format == 'bcf':
+        # Create a index (.csi)
+        call_bcftools(['index', '-c', filename])
+
+    # Report if file cannot be indexed
+    else:
+        raise Exception('Error creating index for: %s. Only .bcf and .vcf.gz (bgzip) files are supported.' % filename)
+
+def convert_to_bcf (filename, output_prefix):
+
+    # Holds the arguments to convert to BCF format
+    convert_args = ['convert', '-O', 'b']
+
+    # Stores the specified output_prefix to the BCF file
+    bcf_output = '%s.bcf' % output_prefix
+
+    # Assigns the output file to the arguments
+    convert_args.extend(['-o', bcf_output])
+
+    # Assigns the specified input to the arguments
+    convert_args.append(filename)
+
+    # Call bcftools
+    call_bcftools(convert_args)
+
+
+def convert_to_vcf (filename, output_prefix):
+
+    # Holds the arguments to convert to VCF format
+    convert_args = ['view', '-O', 'v']
+
+    # Stores the specified output_prefix to the VCF file
+    vcf_output = '%s.vcf' % output_prefix
+
+    # Assigns the output file to the arguments
+    convert_args.extend(['-o', vcf_output])
+
+    # Assigns the specified input to the arguments
+    convert_args.append(filename)
+
+    # Call bcftools
+    call_bcftools(convert_args)
+
+def convert_to_vcfgz (filename, output_prefix):
+
+    # Holds the arguments to convert to VCFGZ format
+    convert_args = ['view', '-O', 'z']
+
+    # Stores the specified output_prefix to the VCFGZ file
+    vcfgz_output = '%s.vcf.gz' % output_prefix
+
+    # Assigns the output file to the arguments
+    convert_args.extend(['-o', vcfgz_output])
+
+    # Assigns the specified input to the arguments
+    convert_args.append(filename)
+
+    # Call bcftools
+    call_bcftools(convert_args)