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 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, "...")