annotate bcftools.py @ 0:3830d29fca6a draft

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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)