def get_fastqc_choice(Fastqc, param):
"""
Function that gets the choice of controling quality of raw input and
filtered data by FastQC.
Takes two arguments : - Fastqc [ElementTree] : subtree which contains the
choice of the user to do or
not a quality control
- param [dict] : dictionnary containing all parameters
Returns param[dict] where the choice for FastQC have been added
"""
# check that the section Fastqc contains only a skip option
if not ce.check_child_number(Fastqc,1):
sys.exit("/!\ The XML file must contain only a skip option in the \
section 'fastqc'!")
# get skip option text
skip = Fastqc.find('skip').text
# check if it's not empty and either 'yes' or 'no'
skip = ce.check_yes_no(skip, 'skip in fastqc')
# if skip = 'no' add to param [dict]
if(skip == 'no') :
param['fastqc']='yes'
return param
def separate_categories_Trimmo(Trimmomatic):
"""
Function that separates the subtree (Trimmomatic program) according to
categories.
Takes one argument : Trimmomatic [ElementTree]
Returns four arguments :
- Adapter [ElementTree] : subtree which contains adapter trimming
parameters
- Quality [ElementTree] : subtree which contains quality trimming
parameters
- Useful [ElementTree] : subtree which contains uselful parameters
"""
# check that the number of categories is 3
if not ce.check_child_number(Trimmomatic,3) :
sys.exit("/!\ The XML file must contain exactly 3 categories for \
Trimmomatic!")
# separates categories of Trimmomatic
for category in Trimmomatic :
# get parameters for 'Adapter-Trimming' in a subtree
if(category.get('name') == 'adapter-trimming') :
Adapter = category
continue
# get parameters for 'Quality-Trimming' in a subtree
elif(category.get('name') == 'quality-trimming') :
Quality = category
continue
# get parameters for 'Usefull-Parameters' in a subtree
elif(category.get('name') == 'useful-parameters') :
Useful = category
continue
else :
sys.exit("/!\ Atleast one category haven't been recognized.\n\
Please, have a look at the name of Trimmomatic categories, atleast one of them \
have been modified.")
return Adapter, Quality, Useful
def separate_steps(root):
"""
Function that separate different steps (Inputs/Outputs and different Programs).
Takes one argument : root [ElementTree] : the root of the tree
Returns three arguments :
- Puts [ElementTree] : subtree which contains inputs and outputs
information's
- Fastqc [ElementTree] : subtree which contains quality control
information's
- Trimmomatic [ElementTree] : subtree which contains Trimmomatic
program parameters
"""
# check that the root have 3 child
if not ce.check_child_number(root,3) :
sys.exit("/!\ Warning : The XML file must contain exactly one Input and\
Output section and two programs (FastQC & Trimmomatic)")
# separte the different steps
for element in root :
if(element.tag == 'input-output') :
Puts = element
elif(element.get('name')=='fastqc') :
Fastqc = element
elif(element.get('name')=='trimmomatic') :
Trimmomatic=element
else:
sys.exit("/!\ Oops! Atleast the name of the section 'input-output' \
or one of program names (fastqc of trimmomatic) have been modified")
return Puts, Fastqc, Trimmomatic
def get_useful_parameters(Useful, param) :
"""
Function that gets useful parameters.
Takes two arguments:
- Useful [ElementTree] : subtree which contains useful parameters
- param [dict] : dictionnary containing all parameters
Returns param [dict] with added quality trimming parameters
"""
# check that useful parameter have 4 child
if not ce.check_child_number(Useful,4):
sys.exit("/!\ The XML file must contain exactly 4 useful parameters.")
# PARAMETERS ---------------------------------------------------------------
for parameter in Useful.findall('parameter') :
# SINGLETON-READS ------------------------------------------------------
if(parameter.get('name') == 'singleton-reads'):
# check if text for show is not empty and either yes or no
show = ce.check_yes_no(parameter.find('show').text,
'show in singleton-reads from useful-parameters')
# if show = yes, then add to the dict
if(show == 'yes'):
param['keep_singleton'] = 'yes'
continue
# CONVERT-TO-PHRED -----------------------------------------------------
elif(parameter.get('name') == 'convert-to-phred') :
# get and check if skip text is not empty and if it's yes or no
skip = ce.check_yes_no(parameter.find('skip').text,
'skip in convert-to-phred from useful parameters')
if(skip == 'no'):
# get parameter
format_num = ce.check_integer(parameter.find('format').text,
'format in convert-to-phred in useful parameters.')
# if format is phred33 or phred64, add to the dict
if(format_num == 33):
param['tophred33'] = 'TOPHRED33'
elif(format_num == 64):
param['tophred64'] = "TOPHRED64"
else :
sys.exit("/!\ Quality score can only be converted to \
phred33 or phred64.")
# THREADS --------------------------------------------------------------
elif (parameter.get('name') == 'threads') :
# get number of threads
number = ce.check_integer(parameter.find('number').text,
'number in threads in useful parameters.')
param['threads'] = number
continue
# COMPRESSION ----------------------------------------------------------
elif(parameter.get('name') == 'compressed-output'):
# get and check if skip text is not empty and if it's yes or no
skip = ce.check_yes_no(parameter.find('skip').text,
'skip in compressed-output from useful parameters.')
if(skip == 'no') :
# get compression format
format = parameter.find('format').text
# check if the text is not empty and lower it
if not empty(format) :
format = format.strip()
format = format.lower()
if(format == '.bz2' or format == '.gz'):
param['compress'] = format
sys.exit("/!\ Value for format in compressed-output in \
useful parameters can only be 'bz2' or 'gz'.")
sys.exit("/!\ You haven't enter a text for format in \
compressed-output in useful parameters.")
continue
else :
sys.exit("You have modified a useful parameter name or enter a new \
one which have not been recognized\n")
return param
def get_quality_parameters(Quality, param) :
"""
Function that gets quality trimming parameters.
Takes 2 arguments:
- Quality [ElementTree] : subtree which contains quality trimming
parameters
- param [dict] : dictionnary containing all parameters
Returns param [dict] with added quality trimming parameters
"""
# check that quality trimming subtree have 9 child (skip and 9 parameters)
if not ce.check_child_number(Quality,9) :
sys.exit("/!\ The XML file must contain exactly one skip option \
skip and 8 parameters for quality trimming.")
# SKIP ---------------------------------------------------------------------
# get the skip option text
skip = Quality.find('skip').text
# check that it is not empty and either 'yes' either 'no'
skip = ce.check_yes_no(skip, 'skip in quality trimming')
# PARAMETERS ---------------------------------------------------------------
# getting the parameters if skip = no
if(skip == 'no'):
param['quality']='yes'
for parameter in Quality.findall('parameter'):
# get and check the skip option for each parameter
param_skip = ce.check_yes_no(parameter.find('skip').text,
'skip in %s from quality trimming'%parameter.get('name'))
# if skip = no, get parameter arguments and add to dict
if(param_skip == 'no'):
# SLIDING-WINDOW -----------------------------------------------
if(parameter.get('name') == 'sliding-window'):
SW_size = ce.check_integer(parameter.find('window-length').text,
'window length in sliding window trimming')
SW_quality = ce.check_integer(parameter.find('required-quality').text,
'required-quality for sliding window trimming')
param['slidingwindow'] = '{0}:{1}'.format(SW_size,SW_quality)
continue
# MAXINFO ------------------------------------------------------
elif(parameter.get('name')== 'maxinfo'):
MI_length = ce.check_integer(parameter.find('target-length').text,
'target-length in maxinfo quality trimming')
MI_strictness = ce.check_float(parameter.find('strictness').text,
'strictness in maxinfo quality trimming')
param['maxinfo'] = '{0}:{1}'.format(MI_length, MI_strictness)
continue
# LEADING ------------------------------------------------------
elif(parameter.get('name') == 'leading'):
lead_quality = ce.check_integer(parameter.find('required-quality').text,
"required-quality in 'leading' quality trimming")
param['leading'] = lead_quality
continue
# TRAILING -----------------------------------------------------
elif(parameter.get('name') == 'trailing'):
tail_quality = ce.check_integer(parameter.find('required-quality').text,
"required-quality in 'trailing' quality trimming")
param['trailing'] = tail_quality
continue
# CROP ---------------------------------------------------------
elif(parameter.get('name') == 'crop'):
crop_length = ce.check_integer(parameter.find('length').text,
"length in 'crop' quality trimming")
param['crop'] = crop_length
continue
# HEADCROP -----------------------------------------------------
elif(parameter.get('name') == 'headcrop'):
headcrop_length = ce.check_integer(parameter.find('length').text,
"length in 'headcrop' quality trimming")
param['headcrop'] = headcrop_length
continue
# MINLEN -------------------------------------------------------
elif(parameter.get('name') == 'minlen'):
min_len = ce.check_integer(parameter.find('length').text,
"length in 'minlen' quality trimming")
param['minlen'] = min_len
continue
# AVERAGE-QUALITY ----------------------------------------------
elif(parameter.get('name') == 'average-quality'):
avg_qual = ce.check_integer(parameter.find('required-quality').text,
"required-quality in 'average quality' trimming")
param['avgqual'] = avg_qual
continue
else :
sys.exit("/!\ You have modified a quality trimming parameter\
name or enter a new one which have not been recognized")
return param
def get_adapter_parameters(Adapter, param):
"""
Function that gets adapter trimming parameters
Takes two arguments:
- Adapter [ElementTree] : subtree which contains adapter trimming
parameters
- param [dict] : dictionnary containing all parameters
Returns param [dict] with added adapter trimming parameters
"""
# check adapter section have 2 child (skip and parameters)
if not ce.check_child_number(Adapter,2):
sys.exit("/!\ Warning : The XML file must contain exactly 1 skip \
option and 1 parameter for adapter trimming.")
# SKIP ---------------------------------------------------------------------
# get the skip option text
skip = Adapter.find('skip').text
# checking if it's not empty and either yes either no
skip = ce.check_yes_no(skip, 'skip in adapter trimming')
# PARAMETERS ---------------------------------------------------------------
# if skip = 'no' get parameters
if(skip == 'no') :
# getting the subtree parameter
parameter = Adapter.find('parameter')
# get parameter which name is 'illuminaclip'
if(parameter.get('name')=='illuminaclip') :
Clip = parameter
# get obligatory parameters ----------------------------------------
fasta_file = ce.check_fasta_file(Clip.find('adapters-fasta-file').text)
mismatches = ce.check_integer(Clip.find('seed-mismatches').text,
'mismatches in illuminaclip')
P_thres = ce.check_integer(Clip.find('palindrome-clip-threshold').text,
'palindrome clip threshold in illuminaclip')
S_thres = ce.check_integer(Clip.find('simple-clip-threshold').text,
'simple clip threshold in illuminaclip')
# optional parameters ----------------------------------------------
# min-adapter-length
minlen = Clip.find('min-adapter-length')
# get min-adapter-length skip value
minlen_skip = ce.check_yes_no(minlen.find('skip').text,
'min-adapter-length skip in adapter trimming')
if(minlen_skip == 'no') :
min_length = ce.check_integer(minlen.find('value').text,
'min-adapter-length in adapter trimming')
else :
min_length = 8 # default value
# get keep-both-reads value
keepreads = Clip.find('keep-both-reads')
# get keep-both-reads skip value
keepreads_skip = ce.check_yes_no(keepreads.find('skip').text,
'keep-both-reads skip in adapter trimming')
if(keepreads_skip == 'no'):
keep = ce.check_true_false(keepreads.find('value').text,
'keep-both-reads in adapter trimming')
else:
keep = 'true' # default value
# Add all parameters to dictionnary --------------------------------
param['illuminaclip']="{0}:{1}:{2}:{3}:{4}:{5}".format(fasta_file,
mismatches,P_thres,
S_thres,min_length,
keep)
# if parameter name is not 'illuminaclip'
else :
sys.exit("/!\ Name of parameter 'illuminaclip' have been modified or\
replaced by something else. Please rename it 'illuminaclip'")
return param