def callFastqMultx(fastq_multx_call_args):
fastq_multx_executable = confirmExecutable('fastq-multx')
# Check if executable is installed
if not fastq_multx_executable:
raise IOError(
'fastq-multx not found. Please confirm the executable is installed'
)
# fastq-multx subprocess call
fastq_multx_call = subprocess.Popen(
[fastq_multx_executable] + fastq_multx_call_args,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE,
preexec_fn=lambda: signal.signal(signal.SIGPIPE, signal.SIG_DFL))
# Get stdout and stderr from subprocess
fastq_multx_stdout, fastq_multx_stderr = fastq_multx_call.communicate()
# Check if code is running in python 3
if sys.version_info[0] == 3:
# Convert bytes to string
fastq_multx_stdout = fastq_multx_stdout.decode()
fastq_multx_stderr = fastq_multx_stderr.decode()
# Check the stderr for errors
checkFastqMultxForErrors(fastq_multx_stderr)
def callBlast(blast_call_args):
# Find the blast executable
blast_executable = confirmExecutable('blastn')
# Check if executable is installed
if not blast_executable:
raise IOError(
'blast not found. Please confirm the executable is installed')
# blast subprocess call
blast_call = subprocess.Popen([blast_executable] + blast_call_args,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
# Get stdout and stderr from subprocess
blast_stdout, blast_stderr = blast_call.communicate()
# Check if code is running in python 3
if sys.version_info[0] == 3:
# Convert bytes to string
blast_stdout = blast_stdout.decode()
blast_stderr = blast_stderr.decode()
# Check the stderr for errors
checkBlastForErrors(blast_stderr)
def test_01_confirmExecutable(self):
# Create list of executables
executable_list = ['vsearch', 'fastq-multx', 'blastn']
# Loop the executables
for executable_str in executable_list:
# Check that the non-standard executables were installed
self.assertIsNotNone(
confirmExecutable(executable_str),
'%s not found. Please install' % executable_str)
# Check that the function fails with a fake executable
self.assertIsNone(
confirmExecutable('retrieve_samples.py' + randomGenerator()))
def callVsearch(vsearch_call_args):
# Find the vsearch executable
vsearch_executable = confirmExecutable('vsearch')
# Check if executable is installed
if not vsearch_executable:
raise IOError(
'vsearch not found. Please confirm the executable is installed')
# vsearch subprocess call
vsearch_call = subprocess.Popen([vsearch_executable] + vsearch_call_args,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
# Get stdout and stderr from subprocess
vsearch_stdout, vsearch_stderr = vsearch_call.communicate()
# Check if code is running in python 3
if sys.version_info[0] == 3:
# Convert bytes to string
vsearch_stdout = vsearch_stdout.decode()
vsearch_stderr = vsearch_stderr.decode()
# Check for errors
checkVsearchForErrors(vsearch_stderr)
def gzipCompress(gzip_filename, return_filename=False, overwrite=True):
# Find the gzip executable
gzip_executable = confirmExecutable('gzip')
# Check if executable is installed
if not gzip_executable:
raise IOError(
'gzip not found. Please confirm the executable is installed')
# Assign the overwrite argument
overwrite_arg = []
# Check if gzip shouldnt overwrite
if overwrite:
# Add the overwrite arg
overwrite_arg.append('-f')
# vsearch subprocess call
gzip_call = subprocess.Popen([gzip_executable, gzip_filename] +
overwrite_arg,
stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
# Get stdout and stderr from subprocess
gzip_stdout, gzip_stderr = gzip_call.communicate()
# Check if code is running in python 3
if sys.version_info[0] == 3:
# Convert bytes to string
gzip_stdout = gzip_stdout.decode()
gzip_stderr = gzip_stderr.decode()
# Update when starting logs
#print(gzip_stdout)
#print(gzip_stderr)
# Check if the filename is to be returned
if return_filename:
return gzip_filename + '.gz'
def executeBackup (backup_executable_str, backup_call_args, backup_output):
# Check if the executable is installed
backup_executable = confirmExecutable(backup_executable_str)
if not backup_executable:
raise IOError(f'{backup_executable_str} not found. Please confirm the executable is installed')
# Open the output file and make the subprocess call
backup_output_file = open(backup_output, 'w')
backup_call = subprocess.Popen([backup_executable] + backup_call_args, stderr = subprocess.PIPE, stdout = backup_output_file)
# Get stdout and stderr from subprocess
backup_stdout, backup_stderr = backup_call.communicate()
if sys.version_info[0] == 3: backup_stderr = backup_stderr.decode()
# Report any errors
if backup_stderr: raise Exception(backup_stderr)
# Close the file
backup_output_file.close()
def pipeBlast(blast_call_args, blast_output, header=None):
# Find the blast executable
blast_executable = confirmExecutable('blastn')
# Check if executable is installed
if not blast_executable:
raise IOError(
'blast not found. Please confirm the executable is installed')
# Open the output file
blast_output_file = open(blast_output, 'w')
# Check if a header was specified
if header:
# Write the head to the output file
blast_output_file.write(header + '\n')
# Flush the file
blast_output_file.flush()
# blast subprocess call
blast_call = subprocess.Popen([blast_executable] + blast_call_args,
stderr=subprocess.PIPE,
stdout=blast_output_file)
# Get stdout and stderr from subprocess
blast_stdout, blast_stderr = blast_call.communicate()
# Check if code is running in python 3
if sys.version_info[0] == 3:
# Convert bytes to string
blast_stderr = blast_stderr.decode()
# Check the stderr for errors
checkBlastForErrors(blast_stderr)
# Close the file
blast_output_file.close()
def __init__(self,
vcf_filename='',
bed_prefix='',
sample_model_dict={},
out_prefix='out',
out_dir='',
**kwargs):
# Check if the plink2 executable was found
self.plink2_path = confirmExecutable('plink2')
if not self.plink2_path:
raise IOError(
'plink2 not found. Please confirm the executable is installed')
self._plink2_call_args = []
self.vcf_filename = vcf_filename
self.bed_prefix = bed_prefix
self.out_prefix = os.path.join(out_dir, out_prefix)
self.out_dir = out_dir
self.sample_model_dict = sample_model_dict
self._files_to_remove = []
# Check if the Binary-Ped files exists
if self.bed_prefix and (os.path.isfile(f'{self.bed_prefix}.bed')
and os.path.isfile(f'{self.bed_prefix}.bim')
and os.path.isfile(f'{self.bed_prefix}.fam')):
self.bed_exists = True
else:
self.bed_exists = False
# Check if the VCF file exists
if self.vcf_filename and os.path.isfile(self.vcf_filename):
self.vcf_exists = True
else:
self.vcf_exists = False
# Prepare the files, if needed
self._prepFiles()