def java_check():
try:
if read_config("Trimmomatic", "java_path").replace(" ", "") == '':
location = subprocess.check_output(['which', 'java'])
else:
location = read_config("Trimmomatic", "java_path")
print "You set the location to: " + mcolor(location)
if location != None:
print "Detected Java program in location: " + mcolor(location)
answer = query_yes_no("Do you want to change the Java Path?", None)
if answer:
location = raw_input("Please enter the Java location: ")
while not (os.path.isfile(location)):
message(1, "Couldn't find any java program!.")
location = raw_input("Please try again: ")
replace_config("Trimmomatic", "java_path", location)
else:
replace_config("Trimmomatic", "java_path", location)
stored_place['java_path'] = location
except subprocess.CalledProcessError:
message(
1,
"\nIt seems you don't have Java in your PATH, Please install and export to the your PATH."
)
message(
4,
"Tip: you can export with following command.[ export PATH=JAVA_LOCATION/java:$PATH ]"
)
except Exception as e:
logging.error(traceback.format_exc())
message(2, "Something is going wrong... please run again. ")
def fastq_path():
try:
title("Please specify the FastQC location")
if read_config("GENERAL", "fastq_path").replace(" ", "") == '':
location = subprocess.check_output(['which', 'fastqc'])
detected = True
else:
location = read_config("GENERAL", "fastq_path")
print "You set the location to: " + mcolor(location)
detected = False
if location != None:
if detected:
print "Detected FastQC program in location: " + mcolor(
location)
answer = query_yes_no("Do you want to change the location?", None)
if answer:
location = raw_input("Please enter the FastQC location: ")
while not (os.path.isfile(location)):
message(1, "Fastq file not found!.")
location = raw_input("Please try again: ")
replace_config("GENERAL", "fastq_path", location)
else:
replace_config("GENERAL", "fastq_path", location)
stored_place['fastq_path'] = location
except subprocess.CalledProcessError:
message(1, "It seems you don't have FastQc in your PATH")
fastq = raw_input("Please enter the FastQC location: ")
while not (os.path.isdir(fastq)):
message(1, "The directory is not exist!.")
fastq = raw_input("Please try again: ")
replace_config("GENERAL", "fastq_path", fastq)
except Exception as e:
logging.error(traceback.format_exc())
message(2, "Something is going wrong... please run again. ")
message(0, "Configuration updated!")
def bedtoolsCheck():
try:
title("Please please specify the bedtools path")
if read_config("Bismark", "bedtools_path").replace(" ", "") == '':
location_bis = subprocess.check_output(['which', 'bedtools'])
detected = True
else:
location_bis = read_config("Bismark", "bedtools_path")
print "You set the location to: " + mcolor(location_bis)
detected = False
if location_bis != None:
if detected:
print "Detected Bedtools program in location: " + mcolor(
location_bis)
answer = query_yes_no("Do you want to change the location?", None)
if answer:
location_bis = raw_input(
"Please enter the bedtools file location: ")
while not (os.path.isfile(location_bis)):
message(1, "The file is not exist!.")
location_bis = raw_input("Please try again: ")
replace_config("Bismark", "bedtools_path", location_bis)
message(4, "--> Configuration updated!")
else:
replace_config("Bismark", "bedtools_path", location_bis)
message(3, "We will keep the default value!")
except subprocess.CalledProcessError:
message(1, "It seems you don't have Bedtools in your PATH")
bismark = raw_input("Please enter the Bedtools file location: ")
while not (os.path.isfile(bismark)):
message(1, "The file is not exist!.")
bismark = raw_input("Please try again: ")
replace_config("Bismark", "bedtools_path", bismark)
message(4, "--> Configuration updated!")
except Exception as e:
logging.error(traceback.format_exc())
message(2, "Something is going wrong... please run again. ")
def confirm(config_section, config_value, mcode):
str_conf = read_config(config_section, config_value)
if not str_conf == '':
if int(mcode == 33):
if str_conf != "true":
str_conf = "'Single-end'."
mcode = 3
else:
str_conf = "'Paired-end'."
mcode = 3
outtxt = true_false_fields_config(str_conf)
if outtxt == "":
outtxt = str_conf
print "The current status is: " + mcolor(outtxt)
# it seems user configured before so asking again to re-config.
answer = query_yes_no("Do you want to re-config this part?", None)
if answer:
return True
else:
message(mcode, "--> Keeping the default value.")
else:
print "Please config parameter ..."
return True
def bismark_path():
try:
title("Alignment parameters (Bismark mapper)")
if read_config("Bismark", "bismark_path").replace(" ", "") == '':
location_bis = subprocess.check_output(['which', 'bismark'])
detected = True
else:
location_bis = read_config("Bismark", "bismark_path")
print "You set the location to: " + mcolor(location_bis)
detected = False
if location_bis != None:
if detected:
print "Detected bismark program in location: " + mcolor(
location_bis)
answer = query_yes_no("Do you want to change the location?", None)
if answer:
location_bis = raw_input("Please enter the Bismark location: ")
while not (os.path.isdir(location_bis)):
message(1, "The directory is not exist!.")
location_bis = raw_input("Please try again: ")
replace_config("Bismark", "bismark_path", location_bis)
message(4, "--> Configuration updated!")
else:
replace_config("Bismark", "bismark_path", location_bis)
message(3, "We will keep the default value!")
except subprocess.CalledProcessError:
message(1, "It seems you don't have Bismark in your PATH")
bismark = raw_input("Please enter the Bismark location: ")
while not (os.path.isdir(bismark)):
message(1, "The directory is not exist!.")
bismark = raw_input("Please try again: ")
replace_config("Bismark", "bismark_path", bismark)
message(4, "--> Configuration updated!")
except Exception as e:
logging.error(traceback.format_exc())
message(2, "Something is going wrong... please run again. ")
'''
Sets the number of parallel instances of Bismark to be run concurrently
'''
title("Configuration part for Bismark Parallel")
if confirm("Bismark", "bis_parallel", 3):
user_input = inputNumber("\nPlease set the number of parallel: ")
replace_config("Bismark", "bis_parallel", user_input)
message(4, "--> Configuration updated!")
else:
pass
'''
Sets buffer size!
'''
title("Configuration part for Bismark buffer Size")
if confirm("Bismark", "buf_size", 3):
user_input = inputNumber(
"\nPlease set the size of buffer (Gigabyte): ")
replace_config("Bismark", "buf_size", user_input)
message(4, "--> Configuration updated!")
else:
pass
'''
Sets nucleotide !
'''
title("Configuration part for Bismark Nucleotide")
message(
4,
"\t**** To change the Nucleotide report option please Enable it.***")
if confirm("Bismark", "nucleotide", 3):
sys.stdout.write(ycolor("\n1") + "-Enable this option.\n")
sys.stdout.write(ycolor("2") + "-Disable this option.\n")
nu_mode = inputNumber("Please enter the number to select:")
while not int(nu_mode) in range(1, 3):
nu_mode = inputNumber("Please enter the valid number:")
if int(nu_mode) == 1:
mode = "true"
else:
mode = "false"
replace_config("Bismark", "nucleotide", mode)
message(4, "--> Configuration updated!")
else:
pass
bedtoolsCheck()
message(0, "Configuration updated for Bismark Mapper!")
def trimmomatic():
# checking for java
java_check()
#
try:
title("Configuration part for Trimmomatic location (location folder)")
if confirm("Trimmomatic", "trim_path", 3):
response = raw_input("Please enter the Trimmomatic location: ")
while not (os.path.isdir(response)):
message(1, "The directory is not exist!.")
response = raw_input("Please enter the Trimmomatic location:")
# searching for jar file!
adap_tosearch = response
list_jar = []
for jarfile in find_file_pattern(adap_tosearch, "*.jar"):
list_jar.append(jarfile)
if len(list_jar) > 1:
message(
1, "There is more than one Jar file in " + adap_tosearch +
" folder.")
message(
2, "Please check directory " + adap_tosearch +
" and re-config again.")
else:
print("Found: " + ycolor(list_jar[0]) + " file.")
replace_config("Trimmomatic", "trim_path", adap_tosearch)
replace_config("Trimmomatic", "trim_jar", list_jar[0])
else:
pass
# find all fasta file from adaptor folder
title("Configuration part for Adapter")
if confirm("Trimmomatic", "name_adap", 3):
adap_tosearch = read_config("Trimmomatic", "trim_path")
list_adaptors = []
for file in find_file_pattern(adap_tosearch + "/adapters/",
"*.fa"):
list_adaptors.append(file)
if len(list_adaptors) == 0:
message(
1, "Could't find any Jar file under " + adap_tosearch +
" folder.")
message(
2, "Please check directory " + adap_tosearch +
" and re-config again.")
else:
print("List of adapters " + adap_tosearch + "/adapters/: \n")
for file in list_adaptors:
sys.stdout.write(
ycolor(str(list_adaptors.index(file))) + " : " + file +
"\n")
response = inputNumber("\nPlease enter the number to select:")
while not int(response) in range(0, len(list_adaptors)):
response = inputNumber("Please enter the valid number:")
response = list_adaptors[int(response)]
replace_config("Trimmomatic", "name_adap", response)
message(4, "--> Configuration updated!")
else:
pass
title("Configuration part for running mode")
if confirm("Trimmomatic", "end_mode", 3):
'''
Paired End or Single End?
'''
sys.stdout.write(ycolor("1") + "-Single-End\n")
sys.stdout.write(ycolor("2") + "-Paired-End\n")
end_mode = inputNumber("\nPlease enter the number to select:")
while not int(end_mode) in range(1, 3):
end_mode = inputNumber("Please enter the valid number:")
mode = ""
if int(end_mode) == 1:
mode = "SE"
else:
mode = "PE"
replace_config("Trimmomatic", "end_mode", mode)
message(4, "--> Configuration updated!")
else:
pass
title("Configuration part for ILLUMINACLIP")
if confirm("Trimmomatic", "ill_clip", 3):
'''
ILLUMINACLIP parameters
'''
user_input = raw_input(
"\nPlease enter the number of ILLUMINACLIP[ " +
read_config("Trimmomatic", "name_adap") + " ]: ")
replace_config("Trimmomatic", "ill_clip", user_input)
message(4, "--> Configuration updated!")
else:
pass
title("Configuration part for LEADING")
if confirm("Trimmomatic", "LEADING", 3):
'''
LEADING parameters
'''
user_input = inputNumber("\nPlease enter the value of LEADING: ")
replace_config("Trimmomatic", "LEADING", user_input)
message(4, "--> Configuration updated!")
else:
pass
title("Configuration part for TRAILING")
if confirm("Trimmomatic", "TRAILING", 3):
'''
TRAILING parameters
'''
user_input = inputNumber("\nPlease enter the value of TRAILING: ")
replace_config("Trimmomatic", "TRAILING", user_input)
message(4, "--> Configuration updated!")
else:
pass
title("Configuration part for SLIDINGWINDOW")
if confirm("Trimmomatic", "SLIDINGWINDOW", 3):
'''
SLIDINGWINDOW parameters
'''
user_input = raw_input(
"\nPlease enter the value of SLIDINGWINDOW: ")
replace_config("Trimmomatic", "SLIDINGWINDOW", user_input)
else:
pass
title("Configuration part for MINLEN")
if confirm("Trimmomatic", "MINLEN", 3):
'''
MINLEN parameters
'''
user_input = inputNumber("\nPlease enter the value of MINLEN: ")
replace_config("Trimmomatic", "MINLEN", user_input)
else:
pass
title("Configuration part for Threading")
if confirm("Trimmomatic", "n_th", 3):
'''
Number of thread to process. there is a default value.
'''
number_thread = inputNumber("\nPlease enter the number of thread:")
replace_config("Trimmomatic", "n_th", number_thread)
else:
pass
message(0, "Configuration Updated!")
except Exception as e:
logging.error(traceback.format_exc(e.message))
message(2, "Something is going wrong... please run again. ")
def result_pipeline():
try:
if confirm("GENERAL", "result_pipeline", 5):
response = raw_input(
"\nPlease enter the result directory."
"\n(we will write all the results inside this folder)"
"\n>> ")
'''
check for permission! is it writable?
'''
while not (os.access(response, os.W_OK)):
try:
os.mkdir(response)
except OSError:
print("Creation of the directory %s failed" % response)
message(
1,
"It seems you don't have permission to write in this directory"
)
response = raw_input("Please enter another location: ")
else:
print("Successfully created the directory %s " % response)
# checking space and warning to user
size = subprocess.check_output(['df', '-Bm', response
]).split()[-3].decode('utf-8')
size = [float(s) for s in re.findall(r'-?\d+\.?\d*', size)]
number_of_dataset = float(
read_config("GENERAL", "number_of_dataset"))
dataset_size = float(read_config("GENERAL", "dataset_size"))
# size per file
if number_of_dataset == 0:
number_of_dataset = 1
per_file = round(dataset_size / number_of_dataset)
print "-----" * 20
print "\nYou have " + mcolor(
size[0]) + " M.byte free space in your disk."
print "The list bellow is recommendation to have Free space in your disk."
print "(This calculation based on your data-set size.)"
print "\nFree space for Trimmomatic part: " + mcolor(
round(per_file * number_of_dataset * 1.2)) + " Gig."
print "Free space for QC-Fastq-report: " + mcolor(
round(2 * number_of_dataset)) + " MB."
print "Free space for Bismark Mapper part: " + mcolor(
round(per_file * number_of_dataset * 1.8)) + " Gig."
print "Free space for Qc-Fastq Bam report: " + mcolor(
round(2 * number_of_dataset)) + " MB."
print "Free space for Bismark Deduplication: " + mcolor(
round(per_file * number_of_dataset * 1.1)) + " Gig."
print "Free space for Bismark Methylation Extractor:" + mcolor(
round(per_file * number_of_dataset * 6)) + " Gig."
print "Free space for Methimpute: " + mcolor(
round(per_file * number_of_dataset * 1.4)) + " Gig."
print "Free space for Other report: " + mcolor(
round(per_file * number_of_dataset * 100)) + " MB."
print bcolors.WARNING + "Note: We recommended at least " \
+ str(number_of_dataset * 10) + " Gigabyte free space." + bcolors.ENDC
print "-----" * 20
stored_place['result_pipeline'] = response
replace_config("GENERAL", "result_pipeline", response)
replace_config("CONFIGPART", "resultdir", "true")
print "creating folders "
subprocess.call(['./src/bash/preparing.sh'])
message(0, "--> Configuration updated! ")
else:
pass
except Exception as e:
logging.error(traceback.format_exc())
message(2, "Something is going wrong... please run again. ")
def raw_dataset():
title("In this part you can specify your data-set location")
print "If you have data-set in pair-end mode, you have to give the pattern of extension.\n"
try:
if confirm("GENERAL", "raw_dataset", 3):
response = raw_input("\nPlease enter the RAW files directory: ")
while not (os.path.isdir(response)):
message(1, "The directory is not exist!.")
response = raw_input("Please enter the RAW files directory: ")
stored_place['raw_dataset'] = response
# check if there is files & give the directory size
list_dataset = find_file_pattern(response, "*.gz")
print "\nFounded " + mcolor(
len(list_dataset)) + " files in the directory."
raw_size = subprocess.check_output(['du', '-h', response
]).split()[-2].decode('utf-8')
size = [float(s) for s in re.findall(r'-?\d+\.?\d*', raw_size)]
replace_config("GENERAL", "dataset_size", size[0])
replace_config("GENERAL", "raw_dataset", response)
replace_config("GENERAL", "number_of_dataset", len(list_dataset))
print "\nAlso, the size of your data-set almost: " + mcolor(
raw_size)
message(4, "--> Configuration updated!")
else:
pass
# detect the pattern if there is pairs file
title("Configuration part for file Pattern")
pairStatus = False
if confirm("GENERAL", "pairs_mode", 33):
# asking for enable /disable
pairStatus = True
print "\nYou can change the default value for your files pattern."
if read_config("GENERAL", "pairs_mode") == "true":
print "Currently you have files in " + ycolor(
"Pair-end case.\n")
else:
print "Currently you have files in " + ycolor(
"Single-end case.\n")
# pring ask enable or disable it
sys.stdout.write(
ycolor("1") + "- You have files in Single-end case.\n")
sys.stdout.write(
ycolor("2") + "- You have files in Pairs-end case.\n")
file_mode = inputNumber("\nPlease enter the number to select:")
while not int(file_mode) in range(1, 3):
file_mode = inputNumber("Please enter the valid number:")
if int(file_mode) == 1:
pairStatus = False
replace_config("GENERAL", "pairs_mode", "false")
replace_config("GENERAL", "first_pattern", "")
replace_config("GENERAL", "secnd_pattern", "")
if pairStatus:
print "--" * 30
print(mcolor("Please specify your data-set pattern. For ex:"))
print(gcolor("XXX_1.fq.gz,\nXXX_2.fq.gz"))
print("First pattern will be: " + mcolor("_1.fq.gz"))
print("And the second pattern is: " + mcolor("_2.fq.gz"))
print "--" * 30
print(mcolor("You can select from default options: "))
sys.stdout.write(
ycolor("1- ") + "XXX" + ycolor("_[1-2].fq.gz") + " format.\n")
sys.stdout.write(
ycolor("2- ") + "XXX" + ycolor("_[1-2].fastq.gz") +
" format.\n")
answer = query_yes_no("Do you want to choice from menu above?",
None)
if answer:
response = inputNumber("\nPlease enter the number to select: ")
while not int(response) in range(1, 3):
response = inputNumber("Please enter the valid number: ")
if int(response) == 1:
pattern_one = "_1.fq.gz"
pattern_two = "_2.fq.gz"
else:
pattern_one = "_1.fastq.gz"
pattern_two = "_2.fastq.gz"
else:
pattern_one = raw_input(
"\nPlease enter the pattern for First pair: ")
pattern_two = raw_input(
"\nPlease enter the pattern for Second pair: ")
replace_config("GENERAL", "pairs_mode", "true")
replace_config("GENERAL", "first_pattern", pattern_one)
replace_config("GENERAL", "secnd_pattern", pattern_two)
# print list of files that we detected by pattern
print("\nFirst pair" + "\t\t" + "Second pair")
print "---" * 10
first_pairs = []
secd_pairs = []
for file_one in find_file_pattern(
read_config("GENERAL", "raw_dataset"), "*" + pattern_one):
first_pairs.append(file_one)
for file_two in find_file_pattern(
read_config("GENERAL", "raw_dataset"), "*" + pattern_two):
secd_pairs.append(file_two)
first_pairs = sorted(first_pairs)
secd_pairs = sorted(secd_pairs)
for item in range(len(first_pairs)):
print first_pairs[item] + "\t\t" + secd_pairs[item]
print ycolor(
"\nPlease check the pairs that listed correctly, otherwise give the different pattern."
)
else:
# skip configuration
pass
message(0, "--> Configuration updated!")
except subprocess.CalledProcessError:
message(
2,
"It seems you don't have permission, please change the directory.")
except Exception as e:
logging.error(traceback.format_exc())
message(2, "Something is going wrong... please run again. ")
def exit():
if (read_config("CONFIGPART", "genomref") == "true"
and read_config("CONFIGPART", "resultdir") == "true"):
replace_config("GENERAL", "firstRun", "false")
pass
def show_config():
print "\n" + "==" * 30
print "Here is summary of configuration parameters: \n"
print "- RAW files location: " + mcolor(
read_config("GENERAL", "raw_dataset"))
print "- Number and Size of the data-set: " + mcolor(read_config("GENERAL", "number_of_dataset"))\
+ " Files and Total size: " + mcolor(read_config("GENERAL", "dataset_size"))+" Gigabyte"
print "- The directory of results: " + mcolor(
read_config("GENERAL", "result_pipeline"))
print "- Genome type: " + mcolor(read_config("GENERAL", "genome_type"))
print "- Genome folder location: " + mcolor(
read_config("GENERAL", "genome_ref"))
print " -- Genome Reference name: " + mcolor(
read_config("GENERAL", "genome_name"))
print "- Paired End: " + mcolor(
true_false_fields_config(read_config("GENERAL", "pairs_mode")))
print "- Trimmomatic location: " + mcolor(
read_config("Trimmomatic", "trim_path"))
print " -- JAVA path: " + mcolor(
read_config("Trimmomatic", "java_path"))
print " -- ILLUMINACLIP: " + mcolor(read_config("Trimmomatic", "name_adap"))\
+":"+mcolor(read_config("Trimmomatic", "ill_clip"))
print " -- LEADING: " + mcolor(read_config("Trimmomatic", "LEADING"))
print " -- TRAILING: " + mcolor(read_config("Trimmomatic", "TRAILING"))
print " -- SLIDINGWINDOW: " + mcolor(
read_config("Trimmomatic", "SLIDINGWINDOW"))
print " -- MINLEN: " + mcolor(read_config("Trimmomatic", "MINLEN"))
print " -- Number of Threads: " + mcolor(
read_config("Trimmomatic", "n_th"))
print "- QC-Fastq path: " + mcolor(read_config("GENERAL", "fastq_path"))
print "- Bismark parameters: " + mcolor(
read_config("Bismark", "bismark_path"))
print " -- Nucleotide status: " + mcolor(
read_config("Bismark", "nucleotide"))
print " -- Number of Parallel: " + mcolor(
read_config("Bismark", "bis_parallel")) + " Threads."
print " -- Buffer size: " + mcolor(read_config(
"Bismark", "buf_size")) + " Gigabyte."
print " -- Samtools Path: " + mcolor(
read_config("Bismark", "samtools_path"))
print " -- Intermediate for MethExtractor: " + mcolor(
true_false_fields_config(read_config("Bismark", "intermediate_files")))
print "- Methylation extraction parameters( Only for quick run)"
print " -- Minimum read coverage: " + mcolor(
read_config("Methimpute", "mincov"))
print "- Methimpute Part:"
print " -- Methimpute Intermediate : " + mcolor(
true_false_fields_config(read_config("Methimpute", "intermediate")))
if (read_config("Methimpute", "intermediate") == "true"):
print " -- Methimpute probability(Intermediate): " + mcolor(
read_config("Methimpute", "intermediate_mode"))
print " -- Methimpute Fit reports: " + mcolor(
true_false_fields_config(read_config("Methimpute", "fit_output")))
print " -- Methimpute Enrichment plots: " + mcolor(
true_false_fields_config(read_config("Methimpute", "enrichment_plot")))
print " -- Methimpute Full report: " + mcolor(
true_false_fields_config(read_config("Methimpute", "full_report")))
print " -- Methimpute Context: " + mcolor(
read_config("Methimpute", "context_report"))
print "- Parallel mode is: " + mcolor(
true_false_fields_config(read_config("GENERAL", "parallel_mode")))
if (read_config("GENERAL", "parallel_mode") == "true"):
print " -- Number of Parallel: " + mcolor(
read_config("GENERAL", "npar")) + " Cores."
print "- E-mail notification: " + mcolor(
true_false_fields_config(read_config("EMAIL", "active")))
if (read_config("EMAIL", "active") == "true"):
print " -- E-mail address: " + mcolor(
read_config("EMAIL", "email_rec"))
message(0, "...")
def methimpute():
if read_config("GENERAL", "genome_type") != "Arabidopsis":
s = "\nWARNING: \nCurrently, genome is NOT A. thaliana, however, your genome is human or any other genome.\n"
s += "Please supply .RData files for generation of metaplots for genes and TEs.\n"
s += "Check manual https://github.com/jlab-code/MethylStar/blob/master/docs/runPipeline.md for more info.\n"
print(ycolor(s))
try:
title("Include Intermediate status")
if confirm("Methimpute", "intermediate", 3):
val = en_di()
replace_config("Methimpute", "intermediate", val)
if val == 'true':
print gcolor("Please specify: independent or constrained ")
sys.stdout.write(ycolor("1") + " - Independent\n")
sys.stdout.write(ycolor("2") + " - Constrained\n")
val = inputNumber("\nPlease enter the number to select:")
while not int(val) in range(1, 3):
val = inputNumber("Please enter a valid number:")
if int(val) == 1:
val = "independent"
elif int(val) == 2:
val = "constrained"
replace_config("Methimpute", "intermediate_mode", val)
else:
replace_config("Methimpute", "intermediate_mode", "false")
message(4, "--> Configuration updated!")
else:
pass
title("Model Fit reports")
if confirm("Methimpute", "fit_output", 3):
val = en_di()
replace_config("Methimpute", "fit_output", val)
message(4, "--> Configuration updated!")
else:
pass
title("Plot Enrichment (Genes, TEs)")
if confirm("Methimpute", "enrichment_plot", 3):
val = en_di()
replace_config("Methimpute", "enrichment_plot", val)
message(4, "--> Configuration updated!")
else:
pass
title("Output full report (Genes, TEs)")
if confirm("Methimpute", "full_report", 3):
val = en_di()
replace_config("Methimpute", "full_report", val)
message(4, "--> Configuration updated!")
else:
pass
title("Run Context: All/ CG| CHG| CHH ")
if confirm("Methimpute", "context_report", 3):
sys.stdout.write(ycolor("1") + " - All\n")
sys.stdout.write(ycolor("2") + " - CG\n")
sys.stdout.write(ycolor("3") + " - CHG\n")
sys.stdout.write(ycolor("4") + " - CHH\n")
val = inputNumber("\nPlease enter the number to select:")
while not int(val) in range(1, 5):
val = inputNumber("Please enter a valid number:")
if int(val) == 1:
val = "All"
elif int(val) == 2:
val = "CG"
elif int(val) == 3:
val = "CHG"
elif int(val) == 4:
val = "CHH"
replace_config("Methimpute", "context_report", val)
message(4, "--> Configuration updated!")
else:
pass
title("Minimum read coverage value (just for quick run)")
if confirm("Methimpute", "mincov", 3):
user_input = raw_input(
"\nPlease enter the value of min.coverage: ")
replace_config("Methimpute", "mincov", user_input)
message(4, "--> Configuration updated!")
else:
pass
message(0, "Configuration Saved!")
except Exception as e:
logging.error(traceback.format_exc())
print(rcolor(e.message))
message(2, "Something is going wrong... please run again. ")
def bismark_path():
try:
title("Alignment parameters (Bismark mapper)")
if read_config("Bismark", "bismark_path").replace(" ", "") == '':
location_bis = subprocess.check_output(['which', 'bismark'])
detected = True
else:
location_bis = read_config("Bismark", "bismark_path")
print "You set the location to: " + mcolor(location_bis)
detected = False
if location_bis != None:
if detected:
print "Detected bismark program in location: " + mcolor(
location_bis)
answer = query_yes_no("Do you want to change the location?", None)
if answer:
location_bis = raw_input("Please enter the Bismark location: ")
while not (os.path.isdir(location_bis)):
message(1, "The directory does not exist!")
location_bis = raw_input("Please try again: ")
replace_config("Bismark", "bismark_path", location_bis)
message(4, "--> Configuration updated!")
else:
replace_config("Bismark", "bismark_path", location_bis)
message(3, "We will keep the default value!")
except subprocess.CalledProcessError:
message(1, "It seems you don't have Bismark in your PATH")
bismark = raw_input("Please enter the Bismark location: ")
while not (os.path.isdir(bismark)):
message(1, "The directory does not exist!")
bismark = raw_input("Please try again: ")
replace_config("Bismark", "bismark_path", bismark)
message(4, "--> Configuration updated!")
except Exception as e:
logging.error(traceback.format_exc())
message(2, "Something is going wrong... please run again. ")
title(
"Running Bismark with paired-end files? pair_1 with unpaired_1 & paired_2 with unpaired_2\n"
)
message(
4,
" ** if you disable then bismark will run pair1 with pair2 and will ignore all unpaired. **\n"
)
if confirm("Bismark", "run_pair_bismark", 3):
val = en_di()
replace_config("Bismark", "run_pair_bismark", val)
message(4, "--> Configuration updated!")
else:
pass
'''
Single cell
'''
title("Run with scBS-Seq (--pbat)? ")
if confirm("Bismark", "single_cell", 3):
val = en_di()
replace_config("Bismark", "single_cell", val)
message(4, "--> Configuration updated!")
else:
pass
if (read_config("Bismark", "single_cell") == "true"):
message(
4,
"\n\t**** A library can only be specified to be either PBAT-Seq library (default) or non-directional. ***"
)
if confirm("Bismark", "directional", 3):
sys.stdout.write(ycolor("1") + "- Default \n")
sys.stdout.write(ycolor("2") + "- --non_directional\n")
val = inputNumber("\nPlease enter the number to select:")
while not int(val) in range(1, 3):
val = inputNumber("Please enter a valid number:")
if int(val) == 2:
txt = "--non_directional"
else:
txt = ""
replace_config("Bismark", "directional", txt)
message(4, "--> Configuration updated!")
else:
replace_config("Bismark", "directional", "")
'''
Sets the number of parallel instances of Bismark to be run concurrently
'''
title("Configuration part for Bismark Parallel")
if confirm("Bismark", "bis_parallel", 3):
user_input = inputNumber("\nPlease set the number of parallel: ")
replace_config("Bismark", "bis_parallel", user_input)
message(4, "--> Configuration updated!")
else:
pass
'''
Sets buffer size!
'''
title("Configuration part for Bismark buffer Size")
if confirm("Bismark", "buf_size", 3):
user_input = inputNumber(
"\nPlease set the size of buffer (Gigabyte): ")
replace_config("Bismark", "buf_size", user_input)
message(4, "--> Configuration updated!")
else:
pass
'''
Sets nucleotide !
'''
title("Configuration part for Bismark Nucleotide")
message(
4,
"\t**** To change the Nucleotide report option please Enable it. ***")
if confirm("Bismark", "nucleotide", 3):
sys.stdout.write(ycolor("\n1") + "-Enable this option.\n")
sys.stdout.write(ycolor("2") + "-Disable this option.\n")
nu_mode = inputNumber("Please enter the number to select:")
while not int(nu_mode) in range(1, 3):
nu_mode = inputNumber("Please enter a valid number:")
if int(nu_mode) == 1:
mode = "true"
else:
mode = "false"
replace_config("Bismark", "nucleotide", mode)
message(4, "--> Configuration updated!")
else:
pass
samtoolsCheck()
bedtoolsCheck()
message(0, "Configuration updated for Bismark Mapper!")
