def __init__(self, FAD, library_type, mark):
self.FAD = FAD
self.library = library_type
self.mark = mark
self.config_object = configparser()
self.genome = self.config_object.get_values("Genome", "genome")
self.annotations = self.config_object.get_values(
"Genome", "annotations")
self.color = Color()
self.min_QUAL = self.config_object.get_values("Call_snp", "min_QUAL")
self.min_DP = self.config_object.get_values("Call_snp", "min_DP")
def __init__(self):
self.devnull = open(os.devnull, 'w')
self.color = Color()
configparser_object = configparser()
self.different_gene_expression = configparser_object.get_bool(
"Operation-switch", "different-gene-expression")
self.allele_specific_expression = configparser_object.get_bool(
"Operation-switch", "allele-specific-expression")
self.alternative_splicing = configparser_object.get_bool(
"Operation-switch", "alternative-splicing")
self.Fusion_gene_analysis = configparser_object.get_bool(
"Operation-switch", "Fusion-gene-analysis")
self.ncRNA_detection_and_analysis = configparser_object.get_bool(
"Operation-switch", "ncRNA-detection-and-analysis")
def __init__(self, FAD, mark):
self.FAD = FAD
self.mark = mark
self.color = Color()
self.config_object = configparser()
self.annotations = self.config_object.get_values(
"Genome", "annotations")
self.genome = self.config_object.get_values("Genome", "genome")
self.blast_db = self.config_object.get_values("nc-RNA", "blast_db")
self.cpc_data_db = self.config_object.get_values(
"nc-RNA", "cpc_data_db")
self.cufflinks_gtf_genome_to_cdna_fasta = self.config_object.get_values(
"nc-RNA", "cufflinks_gtf_genome_to_cdna_fasta")
self.cnci = self.config_object.get_values("nc-RNA", "cnci")
self.run()
def __init__(self, FAD, mark):
self.FAD = FAD
self.mark = mark
self.configparser_object = configparser()
self.genome = self.configparser_object.get_values("Genome", "genome")
self.annotations = self.configparser_object.get_values(
"Genome", "annotations")
self.extract_as = self.configparser_object.get_values(
"Alter-splice", "extract_as")
self.hdrs = self.configparser_object.get_values("Alter-splice", "hdrs")
self.summarize_as = self.configparser_object.get_values(
"Alter-splice", "summarize_as")
self.ea_fpkm = self.configparser_object.get_values(
"Alter-splice", "ea_fpkm")
self.color = Color()
self.run()
def __init__(self, floder_list, threads):
self.color = Color()
self.threads = threads
self.floder_list = floder_list
self.gtf_list_file = os.path.dirname(
self.floder_list[0]) + "/gtf_list_file.txt"
self.cuffmerge_dir = os.path.dirname(
self.floder_list[0]) + "/merged_asm"
self.cuffdiff_dir = os.path.dirname(self.floder_list[0]) + "/diff_out"
self.deseq_out_dir = os.path.dirname(
self.floder_list[0]) + "/deseq_out"
self.deseq_count_dir = os.path.dirname(
self.floder_list[0]) + "/deseq_out/others"
self.deseq_data = os.path.dirname(
self.floder_list[0]) + "/deseq_out/deseq.data"
self.config_object = configparser()
self.annotations = self.config_object.get_values(
"Genome", "annotations")
self.find_diff_p_value = self.config_object.get_values(
"Different_gene_expression", "find_diff_p_value")
self.initialize()
def check_parameters():
global args, comparison, floder_list, config_object, environment, color
environment=Testing_environment()
environment.check()
config_object = configparser()
color = Color()
if "," in args.floder:
comparison=True
floder_list=[get_absolute_path(args.floder.split(",")[0]),get_absolute_path(args.floder.split(",")[1])]
else:
comparison=False
floder_list=[get_absolute_path(args.floder)]
for floder in floder_list:
if not os.path.isdir(floder):
color.fatal_error(floder+" not existed")
if not config_object.has_option("Genome", "genome_index"):
color.print_warning("No genome index(bowtie2) can be found and build the index now")
if environment.check_dependency("bowtie2") == False:
color.fatal_error("External dependency 'bowtie2' not installed.");
shell_cmd='bowtie2-build --threads '+str(int(args.threads)*args.pool)+' '+config_object.get_values("Genome", "genome")+' '+config_object.get_values("Genome", "genome")
run(shell_cmd)
config_object.add_values("Genome", "genome_index", config_object.get_values("Genome", "genome"))
def __init__(self, FAD, comparison, mark):
self.FAD = FAD
self.mark = mark
self.config_object = configparser()
self.fusion_library = self.config_object.get_values(
"Fusion", "fusion_library")
self.bowtie1_index = ""
self.comparison = comparison
self.color = Color()
if comparison:
self.bam_dir = [
self.fusion_library + "/Experimental-Group",
self.fusion_library + "/Control-Group",
self.fusion_library + "/Experimental-Group-Done",
self.fusion_library + "/Control-Group-Done"
]
else:
self.bam_dir = [
self.fusion_library + "/Group",
self.fusion_library + "/Group-Done"
]
self.pre_do()
self.fusion_mapping()