def map_for_contaminating_sequences_one_lib(self, lib_settings):
#first, take unmapped sequences and map them to yeast rRNA, counting mapping stats
if not tps_utils.file_exists(lib_settings.get_rRNA_unmapped_reads()):
subprocess.Popen(
'bowtie2 -f -D 20 -R 3 -N 1 -L 15 -i S,1,0.50 -x %s -p %d -U %s --un-gz %s 2>>%s | samtools view -bS - > %s 2>>%s '
% (
self.experiment_settings.get_rRNA_bowtie_index(),
self.threads,
lib_settings.get_unmappable_reads(),
lib_settings.get_rRNA_unmapped_reads(),
lib_settings.get_rRNA_mapping_stats(),
lib_settings.get_rRNA_mapped_reads(),
lib_settings.get_log(),
),
shell=True).wait()
if not tps_utils.file_exists(lib_settings.get_genome_unmapped_reads()):
#take still unmapped sequences and map them to the rest of the yeast genome, counting mapping stats
subprocess.Popen(
'bowtie2 -f -D 20 -R 3 -N 1 -L 15 -i S,1,0.50 -x %s -p %d -U %s --un-gz %s 2>>%s | samtools view -bS - > %s 2>>%s '
% (
self.experiment_settings.get_genome_bowtie_index(),
self.threads,
lib_settings.get_rRNA_unmapped_reads(),
lib_settings.get_genome_unmapped_reads(),
lib_settings.get_genome_mapping_stats(),
lib_settings.get_genome_mapped_reads(),
lib_settings.get_log(),
),
shell=True).wait()
def map_for_contaminating_sequences_one_lib(self, lib_settings):
# first, take unmapped sequences and map them to yeast rRNA, counting mapping stats
if not tps_utils.file_exists(lib_settings.get_rRNA_unmapped_reads()):
subprocess.Popen(
"bowtie2 -f -D 20 -R 3 -N 1 -L 15 -i S,1,0.50 -x %s -p %d -U %s --un-gz %s 2>>%s | samtools view -bS - > %s 2>>%s "
% (
self.experiment_settings.get_rRNA_bowtie_index(),
self.threads,
lib_settings.get_unmappable_reads(),
lib_settings.get_rRNA_unmapped_reads(),
lib_settings.get_rRNA_mapping_stats(),
lib_settings.get_rRNA_mapped_reads(),
lib_settings.get_log(),
),
shell=True,
).wait()
if not tps_utils.file_exists(lib_settings.get_genome_unmapped_reads()):
# take still unmapped sequences and map them to the rest of the yeast genome, counting mapping stats
subprocess.Popen(
"bowtie2 -f -D 20 -R 3 -N 1 -L 15 -i S,1,0.50 -x %s -p %d -U %s --un-gz %s 2>>%s | samtools view -bS - > %s 2>>%s "
% (
self.experiment_settings.get_genome_bowtie_index(),
self.threads,
lib_settings.get_rRNA_unmapped_reads(),
lib_settings.get_genome_unmapped_reads(),
lib_settings.get_genome_mapping_stats(),
lib_settings.get_genome_mapped_reads(),
lib_settings.get_log(),
),
shell=True,
).wait()
def process_settings(self, settings_file):
"""
- reads the settings file and converts str to float, list, etc.
- stores result in self.settings as a dict()
"""
int_keys = [ 'first_base_to_keep', 'last_base_to_keep', 'max_reads_to_split', 'minimum_reads_for_inclusion',
'pool_5trim', 'pool_3trim', 'min_post_adaptor_length']
#float_keys = []
str_keys = ['adaptor_sequence', 'rrna_index', 'genome_index', 'pool_append', 'pool_prepend', 'primer_sequence']
boolean_keys = ['collapse_identical_reads', 'force_read_resplit', 'force_remapping', 'force_recollapse',
'force_recount', 'force_index_rebuild', 'force_retrim', 'trim_adaptor']
list_str_keys = ['fastq_gz_files', 'sample_names']
#list_float_keys = ['concentrations', 'input_rna']
extant_files = ['pool_fasta',]
config = ConfigParser.ConfigParser()
config.read(settings_file)
settings = {}
for section in config.sections():
for option in config.options(section):
settings[option] = config.get(section, option)
settings[section] = True
for k in int_keys:
settings[k] = int(settings[k])
for k in str_keys:
settings[k] = settings[k]
#for k in float_keys:
# settings[k] = float(settings[k])
for k in boolean_keys:
if not settings[k].lower() in ['true', 'false']:
raise ValueError(
'Boolean value %s must be "true" or "false"' % k)
settings[k] = settings[k].lower() == 'true'
#for k in list_float_keys:
# settings[k] = map(float, simplejson.loads(settings[k]))
#for k in list_int_keys:
# settings[k] = map(int, simplejson.loads(settings[k]))
for k in list_str_keys:
settings[k] = simplejson.loads(settings[k])
self.fqdir = settings['fastq_dir']
self.sample_names = settings['sample_names']
self.fastq_gz_file_handles = [os.path.join(self.fqdir, fastq_gz_file) for fastq_gz_file in
settings['fastq_gz_files']]
for file_handle in self.fastq_gz_file_handles:
assert tps_utils.file_exists(file_handle)
for k in extant_files:
assert tps_utils.file_exists(settings[k])
self.settings = settings
self.wdir = settings['working_dir']
self.rdir = settings['results_dir']
shutil.copy(settings_file, self.rdir)
def get_collapsed_read_fractions(self, lib_settings):
out_name = os.path.join(
self.experiment_settings.get_rdir(), 'QC', 'collapsed_fracs',
'%(sample_name)s.collapsed_read_fractions.pkl' %
{'sample_name': lib_settings.sample_name})
if not tps_utils.file_exists(
out_name) and not self.experiment_settings.get_property(
'force_recollapse'):
collapsed_reads_file = lib_settings.get_collapsed_reads()
read_counts = []
f = gzip.open(collapsed_reads_file)
for line in f:
if not line.strip() == '' and not line.startswith(
'#'): #ignore empty lines and commented out lines
if line.startswith(
'>'): #> marks the start of a new sequence
num_reads = int(line[1:].strip().split('-')[1])
read_counts.append(num_reads)
else:
continue
f.close()
read_fractions = np.array(read_counts) / float(sum(read_counts))
bzUtils.makePickle(read_fractions, out_name)
else:
read_fractions = bzUtils.unPickle(out_name)
return (lib_settings.sample_name, read_fractions)
def get_collapsed_read_fractions(self, lib_settings):
out_name = os.path.join(
self.experiment_settings.get_rdir(),
"QC",
"collapsed_fracs",
"%(sample_name)s.collapsed_read_fractions.pkl" % {"sample_name": lib_settings.sample_name},
)
if not tps_utils.file_exists(out_name) and not self.experiment_settings.get_property("force_recollapse"):
collapsed_reads_file = lib_settings.get_collapsed_reads()
read_counts = []
f = gzip.open(collapsed_reads_file)
for line in f:
if not line.strip() == "" and not line.startswith("#"): # ignore empty lines and commented out lines
if line.startswith(">"): # > marks the start of a new sequence
num_reads = int(line[1:].strip().split("-")[1])
read_counts.append(num_reads)
else:
continue
f.close()
read_fractions = np.array(read_counts) / float(sum(read_counts))
bzUtils.makePickle(read_fractions, out_name)
else:
read_fractions = bzUtils.unPickle(out_name)
return (lib_settings.sample_name, read_fractions)
def sequence_counts_exist(self):
sequence_counts = self.get_sequence_counts()
return tps_utils.file_exists(sequence_counts)
def mapped_reads_exist(self):
mapped_reads = self.get_mapped_reads()
return tps_utils.file_exists(mapped_reads)
def trimmed_reads_exist(self):
trimmed_reads = self.get_trimmed_reads()
return tps_utils.file_exists(trimmed_reads)
def primerless_reads_exist(self):
primerless_reads = self.get_primer_trimmed_reads()
return tps_utils.file_exists(primerless_reads)
def adaptorless_reads_exist(self):
adaptorless_reads = self.get_adaptor_trimmed_reads()
return tps_utils.file_exists(adaptorless_reads)
def collapsed_reads_exist(self):
collapsed_reads = self.get_collapsed_reads()
return tps_utils.file_exists(collapsed_reads)
def split_reads_exist(self):
split_reads = self.get_split_reads()
return tps_utils.file_exists(split_reads)
def bowtie_index_exists(self):
return tps_utils.file_exists(self.get_bowtie_index()+'.1.bt2')
