def __init__(self, working_directory, sample_type, thread, fastq_list,
info_dict, map_type):
self.working_directory = working_directory
self.thread = thread
self.sample_type = sample_type
self.map_type = map_type
self.info_dict = info_dict
self.fastq_list = fastq_list
self.file_list = []
self.paths = GetPaths()
os.chdir(self.working_directory)
def __init__(self, working_directory, map_type, sample_type, library_matching_id, thrds, issplitchr):
self.get_paths = GetPaths()
self.main_directory = working_directory
self.folder_directory = working_directory + "/" + map_type
self.working_directory = working_directory + "/" + map_type + "/Mapping"
self.map_type = map_type
self.sample_type = sample_type
self.library_matching_id = library_matching_id
self.threads = thrds
self.bundle_dir = self.get_paths.ref_dir + "hg19_bundle"
self.split_chr = issplitchr
self.file_list = []
os.chdir(self.working_directory)
def __init__(self, working_directory, map_type, sample_type,
library_matching_id, thrds, gatk_tools):
self.get_paths = GetPaths()
self.working_directory = working_directory
self.map_type = map_type
self.sample_type = sample_type
self.library_matching_id = library_matching_id
self.threads = thrds
self.bundle_dir = self.get_paths.ref_dir + "hg19_bundle"
self.gatk_tools = False
if gatk_tools == "Yes":
self.gatk_tools = True
else:
self.gatk_tools = False
os.chdir(self.working_directory)
def __init__(self, variant_annotater, wd, sample_name, thread_v, will_annotate, annotate_all):
self.get_paths = GetPaths()
self.working_directory = wd
os.chdir(self.working_directory)
print(self.working_directory)
self.sample_name = sample_name
self.v_annotater = variant_annotater
self.threads = str(thread_v)
if annotate_all:
self.annotate_files = glob.glob("*.vcf")
else:
self.annotate_files = will_annotate
self.humandb = self.get_paths.annovar + "humandb_38/"
self.xref = self.get_paths.annovar + "example/gene_fullxref.txt"
self.annovar_dir = self.get_paths.annovar + "table_annovar.pl"
self.file_list = []
def __init__(self, working_directory, map_type, sample_type,
library_matching_id, thrds, trim):
"""
Parameters
----------
working_directory : str
The folder directory of where fastq files are in
map_type : str
Mapping algorithm decision: Bwa or Bowtie2
sample_type : str
Type of sample: Tumor or Germline
library_matching_id : str
ID of patient which own the sample
thrds : str
Number of cores that wanted to use
bundle_dir : str
Path directory for reference files
file_list : str
List of files that created in this step
trim : str
"Yes" or "No" option must be used. Use "Yes" in order to trim fastq files.
"""
self.get_paths = GetPaths(
) # Get paths of algorithms inside paths.py module
if working_directory[-1] == "/" or working_directory[-1] == "\\":
self.working_directory = working_directory[:-1]
else:
self.working_directory = working_directory
self.map_type = map_type
self.sample_type = sample_type
self.library_matching_id = library_matching_id
self.threads = str(
thrds) # in case of given as integer it convert to string
#self.bundle_dir = self.get_paths.ref_dir + "hg19_bundle" # contains reference bundle
self.bundle_dir = self.get_paths.ref_dir # contains reference bundle
self.folder_directory = self.working_directory
if trim == "Yes":
self.trim = True
self.working_directory = self.working_directory + "/QC"
else:
self.trim = False
self.file_list = []
self.delete_file_list = []
os.chdir(self.working_directory)
def __init__(self,
variant_caller,
thrds,
map_type,
germline_bam,
wd,
tumor_bam,
sample_name,
tumor_only,
tumor_interval=None,
germline_interval=None):
self.get_paths = GetPaths(
) # Get paths of algorithms inside paths.py module
self.working_directory = wd
up_dir = str(self.working_directory).split("/")[:-1]
self.folder_directory = "/".join(up_dir)
os.chdir(self.working_directory)
print(self.working_directory)
self.v_caller = variant_caller
self.map_type = map_type
self.output_name = self.map_type + "_" + self.v_caller + "_" + sample_name
self.threads = str(thrds)
self.ref_dir = self.get_paths.ref_dir + "Homo_sapiens_assembly38.fasta" # contains reference files
self.tumor_bam = tumor_bam
self.germline_bam = germline_bam
if tumor_only == "Yes":
self.tumor_only_mode = True
else:
self.tumor_only_mode = False
# If selected variant caller is Mutect2 from GATK3
if variant_caller == "Mutect2_gatk3":
self.tumor_interval = tumor_interval
self.germline_interval = germline_interval
self.realign_target = self.tumor_interval + " " + self.germline_interval
def __init__(self, folder):
self.folder = folder
self.get_paths = GetPaths()
self.ref_dir = self.get_paths.ref_dir + "Homo_sapiens_assembly38.fasta"
def create_index(lastbam, function, threads, step):
indexcol = "java -Dpicard.useLegacyParser=false -jar " + GetPaths(
).picard_path + " BuildBamIndex -I " + lastbam
log_command(indexcol, function, threads, step)
return lastbam[:-3] + "bai"
def __init__(self, normal_file, normal_target_interval):
self.get_paths = GetPaths()
self.normal_bam = normal_file
self.normal_interval = normal_target_interval
self.output_vcf = "output." + str(self.normal_bam).split("/")
def create_index(lastbam, function, threads, step):
indexcol = "java -jar " + GetPaths(
).picard_path + " BuildBamIndex I=" + lastbam
log_command(indexcol, function, threads, step)
return lastbam[:-3] + "bai"