def run_BWA_Command_for_RAD(genome_file,
fastq_file1,
fastq_file2=None,
output_dir=None,
sample_name=None,
clean_up=True,
thread=1,
read_group=None,
illumina=False,
fifo=False):
run_fine = True
try:
pipeline_param = utils_param.get_pipeline_parameters()
BWA_dir = pipeline_param.get_bwa_dir()
samtools_dir = pipeline_param.get_samtools_dir()
picard_dir = pipeline_param.get_picard_dir()
#get the path to the current script to infer the path to RAD_set_read1_consensus_to_read2.py
script_dir = os.path.dirname(os.path.realpath(__file__))
path_to_script = os.path.join(script_dir,
"RAD_set_read1_consensus_to_read2.py")
if not os.path.exists(path_to_script):
logging.warning(
"Can't find RAD_set_read1_consensus_to_read2.py which is required"
)
path_to_script = "RAD_set_read1_consensus_to_read2.py"
except Config_file_error, e:
#logging.exception('Config_file_error:')
logging.critical(
"You need to have the environment variable properly set to use that script"
)
return False
def run_stats_from_bam(bam_file):
try:
pipeline_param = utils_param.get_pipeline_parameters()
samtools_dir = pipeline_param.get_samtools_dir()
except Config_file_error, e:
logging.warning("You'll need to have samtools in your path")
samtools_dir = ''
def run_stats_from_bam(bam_file):
try:
pipeline_param=utils_param.get_pipeline_parameters()
samtools_dir=pipeline_param.get_samtools_dir()
except Config_file_error, e:
logging.warning("You'll need to have samtools in your path")
samtools_dir=''
def prepare_genome(genome_file, color_space=False):
run_fine = True
pipeline_param = utils_param.get_pipeline_parameters()
BWA_dir = pipeline_param.get_bwa_dir()
BWA_bin = os.path.join(BWA_dir, 'bwa')
genome_loader = GenomeLoader(genome_file=genome_file)
length = 0
for fasta_rec in genome_loader:
header, sequence = fasta_rec
length += len(sequence)
if length > 1000000000:
break
genome_loader.close()
#Following recommendation set the indexing algorithm to is if genome is <10M
if length > 1000000000:
a_option = 'bwtsw'
else:
a_option = 'is'
#Create the indexes
if color_space:
command = '%s index -c -a %s %s' % (BWA_bin, a_option, genome_file)
else:
command = '%s index -a %s %s' % (BWA_bin, a_option, genome_file)
command_runner.run_command(command)
return run_fine
def prepare_genome(genome_file,color_space=False):
run_fine=True
pipeline_param=utils_param.get_pipeline_parameters()
BWA_dir=pipeline_param.get_bwa_dir()
BWA_bin=os.path.join(BWA_dir,'bwa')
genome_loader = GenomeLoader(genome_file=genome_file)
length=0
for fasta_rec in genome_loader:
header, sequence = fasta_rec
length+=len(sequence)
if length>1000000000:
break
genome_loader.close()
#Following recommendation set the indexing algorithm to is if genome is <10M
if length>1000000000:
a_option='bwtsw'
else:
a_option='is'
#Create the indexes
if color_space:
command='%s index -c -a %s %s'%(BWA_bin, a_option, genome_file)
else:
command='%s index -a %s %s'%(BWA_bin, a_option, genome_file)
command_runner.run_command(command)
return run_fine
def get_mpileup_from_bam(bam_file, options=''):
try:
pipeline_parm=utils_param.get_pipeline_parameters()
samtools_bin=os.path.join(pipeline_parm.get_samtools_dir(),'samtools')
except Config_file_error, e:
logging.warning("Can't find the configuration file you'll need to have samtools in you path.")
samtools_bin='samtools'
def index_bam_file(bam_file, samtools_bin=None):
if samtools_bin==None:
try:
pipeline_parm=utils_param.get_pipeline_parameters()
samtools_bin=os.path.join(pipeline_parm.get_samtools_dir(),'samtools')
except Config_file_error, e:
logging.warning("Can't find the configuration file you'll need to have samtools in you path.")
samtools_bin='samtools'
def RAD_median_coverage(bam_files,output_file):
try:
pipeline_param=utils_param.get_pipeline_parameters()
samtools_dir=pipeline_param.get_samtools_dir()
except Config_file_error, e:
#logging.exception('Config_file_error:')
logging.warning("You'll need to have samtools in your path")
samtools_dir=''
def set_read1_consensus_to_read2_old(input_bam_file, output_bam_file):
try:
pipeline_param=utils_param.get_pipeline_parameters()
samtools_dir=pipeline_param.get_samtools_dir()
except Config_file_error, e:
#logging.exception('Config_file_error:')
logging.critical("You need to have the environment variable properly set to use that script")
return False
def mark_duplicate(bam_file, distance_threshold=5):
try:
pipeline_param = utils_param.get_pipeline_parameters()
samtools_dir = pipeline_param.get_samtools_dir()
picard_dir = pipeline_param.get_picard_dir()
except Config_file_error, e:
logging.warning("You'll need to have samtools in your path")
samtools_dir = ''
picard_dir = None
def run_alignment(consensus_file, read1_fastq, read2_fastq, single_fastq, all_read_groups, snp_call=False):
try:
pipeline_param = utils_param.get_pipeline_parameters()
picard_dir = pipeline_param.get_picard_dir()
# GATK_dir=pipeline_param.get_gatk_dir()
samtools_dir = pipeline_param.get_samtools_dir()
except Config_file_error, e:
logging.exception('Config_file_error:')
sys.exit(1)
def mark_duplicate(bam_file, distance_threshold=5):
try:
pipeline_param=utils_param.get_pipeline_parameters()
samtools_dir=pipeline_param.get_samtools_dir()
picard_dir=pipeline_param.get_picard_dir()
except Config_file_error, e:
logging.warning("You'll need to have samtools in your path")
samtools_dir=''
picard_dir=None
def get_sam_stream(bam_file, samtools_bin=None, options='', chomosome_and_position=''):
"""This method opens a .bam file with samtools and returns an open file. The std error will be output in the console through another thread."""
if samtools_bin==None:
try:
pipeline_parm=utils_param.get_pipeline_parameters()
samtools_bin=os.path.join(pipeline_parm.get_samtools_dir(),'samtools')
except Config_file_error, e:
logging.warning("Can't find the configuration file you'll need to have samtools in you path.")
samtools_bin='samtools'
def get_mpileup_from_bam(bam_file, options=''):
try:
pipeline_parm = utils_param.get_pipeline_parameters()
samtools_bin = os.path.join(pipeline_parm.get_samtools_dir(),
'samtools')
except Config_file_error, e:
logging.warning(
"Can't find the configuration file you'll need to have samtools in you path."
)
samtools_bin = 'samtools'
def index_bam_file(bam_file, samtools_bin=None):
if samtools_bin == None:
try:
pipeline_parm = utils_param.get_pipeline_parameters()
samtools_bin = os.path.join(pipeline_parm.get_samtools_dir(),
'samtools')
except Config_file_error, e:
logging.warning(
"Can't find the configuration file you'll need to have samtools in you path."
)
samtools_bin = 'samtools'
def run_all_snps_call(directory):
directory = os.path.abspath(directory)
all_dirs = glob(os.path.join(directory, '*_dir'))
GATK_dir = None
try:
pipeline_param = utils_param.get_pipeline_parameters()
picard_dir = pipeline_param.get_picard_dir()
GATK_dir = pipeline_param.get_gatk_dir()
samtools_dir = pipeline_param.get_samtools_dir()
samtools_bin = os.path.join(samtools_dir, 'samtools')
except Config_file_error, e:
logging.exception('Config_file_error:')
sys.exit(1)
def run_all_snps_call(directory):
directory = os.path.abspath(directory)
all_dirs = glob(os.path.join(directory, '*_dir'))
GATK_dir = None
try:
pipeline_param = utils_param.get_pipeline_parameters()
picard_dir = pipeline_param.get_picard_dir()
GATK_dir = pipeline_param.get_gatk_dir()
samtools_dir = pipeline_param.get_samtools_dir()
samtools_bin = os.path.join(samtools_dir, 'samtools')
except Config_file_error, e:
logging.exception('Config_file_error:')
sys.exit(1)
def run_alignment(consensus_file,
read1_fastq,
read2_fastq,
single_fastq,
all_read_groups,
snp_call=False):
try:
pipeline_param = utils_param.get_pipeline_parameters()
picard_dir = pipeline_param.get_picard_dir()
# GATK_dir=pipeline_param.get_gatk_dir()
samtools_dir = pipeline_param.get_samtools_dir()
except Config_file_error, e:
logging.exception('Config_file_error:')
sys.exit(1)
def run_BWA_Command(genome_file, fastq_file1, fastq_file2=None, output_dir=None, sample_name=None,
clean_up=True, sort=False, thread=1, analysis_type=None, read_group=None, illumina=False):
run_fine=True
try:
pipeline_param=utils_param.get_pipeline_parameters()
BWA_dir=pipeline_param.get_bwa_dir()
samtools_dir=pipeline_param.get_samtools_dir()
picard_dir=pipeline_param.get_picard_dir()
except Config_file_error, e:
logging.exception('Config_file_error:')
logging.warning("You'll need to have bwa and samtools in your path")
BWA_dir=''
samtools_dir=''
picard_dir=None
def get_sam_stream(bam_file,
samtools_bin=None,
options='',
chomosome_and_position=''):
"""This method opens a .bam file with samtools and returns an open file. The std error will be output in the console through another thread."""
if samtools_bin == None:
try:
pipeline_parm = utils_param.get_pipeline_parameters()
samtools_bin = os.path.join(pipeline_parm.get_samtools_dir(),
'samtools')
except Config_file_error, e:
logging.warning(
"Can't find the configuration file you'll need to have samtools in you path."
)
samtools_bin = 'samtools'
def run_BWA_Command_for_RAD(genome_file, fastq_file1, fastq_file2=None, output_dir=None, sample_name=None,
clean_up=True, thread=1, read_group=None, illumina=False, fifo=False):
run_fine=True
try:
pipeline_param=utils_param.get_pipeline_parameters()
BWA_dir=pipeline_param.get_bwa_dir()
samtools_dir=pipeline_param.get_samtools_dir()
picard_dir=pipeline_param.get_picard_dir()
#get the path to the current script to infer the path to RAD_set_read1_consensus_to_read2.py
script_dir = os.path.dirname(os.path.realpath(__file__))
path_to_script = os.path.join(script_dir,"RAD_set_read1_consensus_to_read2.py")
if not os.path.exists(path_to_script):
logging.warning("Can't find RAD_set_read1_consensus_to_read2.py which is required")
path_to_script = "RAD_set_read1_consensus_to_read2.py"
except Config_file_error, e:
#logging.exception('Config_file_error:')
logging.critical("You need to have the environment variable properly set to use that script")
return False
def run_BWA_Command(genome_file,
fastq_file1,
fastq_file2=None,
output_dir=None,
sample_name=None,
clean_up=True,
sort=False,
thread=1,
analysis_type=None,
read_group=None,
illumina=False):
run_fine = True
try:
pipeline_param = utils_param.get_pipeline_parameters()
BWA_dir = pipeline_param.get_bwa_dir()
samtools_dir = pipeline_param.get_samtools_dir()
picard_dir = pipeline_param.get_picard_dir()
except Config_file_error, e:
logging.exception('Config_file_error:')
logging.warning("You'll need to have bwa and samtools in your path")
BWA_dir = ''
samtools_dir = ''
picard_dir = None