def __init__(self, settings_file):

self.settings_file = settings_file

self.process_settings(settings_file)

self.rRNA_seqs = mod_utils.convertFastaToDict(self.get_rRNA_fasta())

def get_force_recount(self, count_type):

return self.settings['force_%s_recount' % count_type]

def get_settings_file(self):

return self.settings_file

def get_property(self, property, default=None):

try:

if not property in self.settings and default != None:

return default

return self.settings[property]

except:

print self.settings

raise ValueError('cannot find %s' % property)

def get_rdir(self):

mod_utils.make_dir(self.rdir)

return self.rdir

def get_wdir(self):

mod_utils.make_dir(self.wdir)

return self.wdir

def iter_lib_settings(self):

for i in range(len(self.sample_names)):

yield mod_lib_settings(self,

self.sample_names[i],

self.fastq_gz_file_handles[i])

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', 'min_post_adaptor_length', 'min_base_quality', 'min_mapping_quality']

float_keys = ['confidence_interval_cutoff', 'fold_change_cutoff', 'winsorization_upper_limit']

str_keys = ['adaptor_sequence', 'rrna_fasta', 'experiment_name', 'affected_nucleotides', 'pymol_base_script', 'pymol_base_script_colorchange', 'tptn_file_18s', 'tptn_file_25s']

boolean_keys = ['make_interactive_plots']

list_str_keys = ['fastq_gz_files', 'sample_names', 'experimentals', 'no_mod_controls', 'with_mod_controls', 'exclude_constitutive']

#list_float_keys = ['probe_concentrations']

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.experimentals = settings['experimentals']

self.no_mod_controls = settings['no_mod_controls']

self.with_mod_controls = settings['with_mod_controls']

self.exclude_constitutive = settings['exclude_constitutive']

try:

assert len(self.experimentals) == len(self.no_mod_controls)

assert len(self.experimentals) == len(self.with_mod_controls)

except:

print 'error: experimentals, no_mod_controls, and with_mod_controls should all be the same length'

print 'for mutation rate purposes, its ok to reuse a dataset here, it really doesnt matter'

try:

for sample_name in self.experimentals+self.no_mod_controls+self.with_mod_controls:

assert sample_name in self.sample_names

except:

print sample_name, ' not in sample names, make sure you are using regular quotation marks'

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 mod_utils.file_exists(file_handle)

self.settings = settings

self.rdir = settings['results_dir']

mod_utils.make_dir(self.rdir)

shutil.copy(settings_file, self.rdir)

def get_rRNA_fasta(self):

return self.get_property('rrna_fasta')

def get_star_index(self):

index = os.path.join(

self.get_rdir(),

'star_index')

return index

def star_index_exists(self):

star_index = self.get_star_index()

return mod_utils.file_exists(star_index)

def get_log(self):

log = os.path.join(

self.get_rdir(),

'log.txt')

return log

def write_to_log(self, text, add_time = True):

f = open(self.get_log(), 'a')

now = datetime.datetime.now()

time = now.strftime("%Y-%m-%d %H:%M")

if add_time:

f.write('[%s] %s\n' % (time, text))

else:

f.write(text)

f.close()

def get_shapemapper_config_file(self):

fname = os.path.join(

self.get_rdir(),

'trimmed_reads',

'shapemapper_settings.cfg')

def __init__(self, experiment_settings, sample_name, fastq_gz_filehandle):

self.experiment_settings = experiment_settings

self.sample_name = sample_name

self.fastq_gz_filehandle = fastq_gz_filehandle

def get_property(self, property):

return self.experiment_settings.get_property(property)

def get_log(self):

mod_utils.make_dir(os.path.join(self.experiment_settings.get_rdir(), 'logs'))

log = os.path.join(

self.experiment_settings.get_rdir(),

'logs',

'%(sample_name)s.log' %

{'sample_name': self.sample_name})

return log

def write_to_log(self, text, add_time = True):

f = open(self.get_log(), 'a')

now = datetime.datetime.now()

time = now.strftime("%Y-%m-%d %H:%M")

if add_time:

f.write('[%s] %s\n' % (time, text))

else:

f.write(text)

f.close()

def get_fastq_file(self):

return self.fastq_gz_filehandle

def get_adaptor_trimmed_reads(self, prefix_only=False):

if prefix_only:

trimmed_reads = os.path.join(

self.experiment_settings.get_rdir(),

'adaptor_removed',

'%(sample_name)s' %

{'sample_name': self.sample_name})

else:

trimmed_reads = os.path.join(

self.experiment_settings.get_rdir(),

'adaptor_removed',

'%(sample_name)s-trimmed.fastq.gz' %

{'sample_name': self.sample_name})

return trimmed_reads

def get_trimmed_reads(self):

trimmed_reads = os.path.join(

self.experiment_settings.get_rdir(),

'trimmed_reads',

'%(sample_name)s.trimmed.fastq.gz' %

{'sample_name': self.sample_name})

return trimmed_reads

def get_shapemapper_out_dir(self):

shapemapper_out = os.path.join(

self.experiment_settings.get_rdir(),

'shapemapper',

'%(sample_name)s_out' %

{'sample_name': self.sample_name})

return shapemapper_out

def get_shapemapper_log(self):

shapemapper_out = os.path.join(

self.experiment_settings.get_rdir(),

'shapemapper',

'%(sample_name)s_out' %

{'sample_name': self.sample_name}, '%(sample_name)s_shapemapper.log' %

{'sample_name': self.sample_name})

return shapemapper_out

def get_shapemapper_temp_dir(self):

shapemapper_temp = os.path.join(

self.experiment_settings.get_rdir(),

'shapemapper',

'%(sample_name)s_temp' %

{'sample_name': self.sample_name})

return shapemapper_temp

def get_counting_prefix(self):

return os.path.join(

self.experiment_settings.get_rdir(),

'read_counts',

'%(sample_name)s' %

{'sample_name': self.sample_name})

def get_mapped_reads_prefix(self):

mapped_reads = os.path.join(self.experiment_settings.get_rdir(), 'mapped_reads',

'%(sample_name)s' % {'sample_name': self.sample_name})

return mapped_reads

def get_mapped_reads(self):

mapped_reads = '%(prefix)sAligned.sortedByCoord.out.bam' % {'prefix': self.get_mapped_reads_prefix()}

return mapped_reads

def get_5p_count_wig(self):

wig = '%(prefix)sSignal.Unique.str1.out.wig' % {'prefix': self.get_mapped_reads_prefix()}

return wig

def read_5p_counts_exists(self):

return mod_utils.file_exists(self.get_read_5p_counts())

def get_mutation_counts(self):

return os.path.join(

self.experiment_settings.get_rdir(),

'read_counts',

'%(sample_name)s.mutations.pkl' %

{'sample_name': self.sample_name})

def mutation_counts_exists(self):

return mod_utils.file_exists(self.get_mutation_counts())

def adaptorless_reads_exist(self):

adaptorless_reads = self.get_adaptor_trimmed_reads()

return mod_utils.file_exists(adaptorless_reads)

def trimmed_reads_exist(self):

trimmed_reads = self.get_trimmed_reads()

return mod_utils.file_exists(trimmed_reads)

def mapped_reads_exist(self):

mapped_reads = self.get_mapped_reads()