def Byte_Fill(str0):
str1 = convert_7D(str0)
str2 = convert_7E(str1)
str3 = convert_1X(str2)
str4 = convert_0X(str3)
return str4
if __name__ == "__main__":
InfoString = ""
ini_path = "./Byte_Fill_data.ini"
if len(sys.argv) == 2:
ini_path = sys.argv[1]
InfoString = readConfigFile.readConfigFile(ini_path, "InfoString",
InfoString)
InfoString = InfoString[:16]
print(len(InfoString))
print("-------------字节填充之后的数据信息-------------")
Fill_string = Byte_Fill(InfoString)
print(Fill_string)
print("-------------帧首部的四部分---------------------")
print("帧起始标志:7E ", "A:FF ", "C:03 ", "协议：0021 或 C021 或 8021")
print("-------------帧尾部的两部分---------------------")
print("FCS:XX ", "帧结束标志：7E")
print("-------------字节填充后的发送帧为---------------")
print("若为IP数据报： " + "7E FF 03 0021", Fill_string, " XX",
" 7E")
print("若为ppp链路控制协议LCP的数据：", "7E FF 03 C021 ", Fill_string, " XX", " 7E")
print("若为网络层的控制数据： ", "7E FF 03 8021 ", Fill_string, " XX", " 7E")
print("-------------字节删除后的接收帧为---------------")
def restart(programDirectory, step, project, status):
(working_dir, available_tools, account, exclude, modules, recursive) = readConfigFile.readConfigFile(
programDirectory
)
statusFiles = ["timeout", "failed", "cancelled"]
processes = {
"caller": ["annotation", "filter", "database", "combine", "cleaning"],
"combine": ["annotation", "filter", "database", "combine", "cleaning"],
"db": ["annotation", "filter", "database", "cleaning"],
"filter": ["annotation", "filter", "cleaning"],
"annotation": ["annotation", "cleaning"],
}
default_working_dir = working_dir
print ("Restarting:")
projects = {}
# all projects found in the project dictionary are being analysed
for file in os.listdir(os.path.join(programDirectory, "projects")):
if file.endswith(".txt") and not file.endswith("example.txt"):
with open(os.path.join(programDirectory, "projects", file)) as ongoing_fd:
projectID = file.split("/")[-1]
projectID = file.replace(".txt", "")
# if the user has selected a project manually, and it is not this one
# then there is really nothing to do.
if not (project and (project != projectID)):
projects[projectID] = {}
for line in ongoing_fd:
try:
if line[0] != "#":
info = line.strip()
info = info.split("\t")
projects[projectID][info[0]] = info[1:]
except:
# the pipeline should not crash if the user adds some newlines etc to the project file
pass
# check if any status file is selected
restartStatusFiles = []
if status:
if status == "all":
restartStatusFiles = statusFiles
elif status in statusFiles:
restartStatusFiles = [status]
else:
print ("Invalid status file.")
return 0
# check which caller is selected
callerToBeRestarted = []
if "caller" in step:
if step["caller"] == "all":
print ("All callers are being restarted!")
for tools in available_tools:
callerToBeRestarted.append(tools)
else:
if step["caller"] in available_tools:
callerToBeRestarted.append(step["caller"])
print "Restarting caller {}.".format(step["caller"])
# restart the callers by removing the status files
for project in projects:
if not projects[project]["output"]:
working_dir = default_working_dir
else:
working_dir = projects[project]["output"][0]
for caller in callerToBeRestarted:
deletedProcess = os.path.join(working_dir, project, "process", caller)
if os.path.exists(deletedProcess) and not restartStatusFiles:
shutil.rmtree(deletedProcess)
# if a certain statusfile is specified, restart only that file
elif restartStatusFiles:
for files in restartStatusFiles:
deletedStatusFile = os.path.join(deletedProcess, "calling", files)
if os.path.exists(deletedStatusFile):
os.remove(deletedStatusFile)
# Check which steps will be restarted
processToBeRestarted = []
if "caller" in step:
processToBeRestarted = processes["caller"]
elif "combine" in step:
processToBeRestarted = processes["combine"]
elif "db" in step:
processToBeRestarted = processes["db"]
elif "filter" in step:
processToBeRestarted = processes["filter"]
elif "annotation" in step:
processToBeRestarted = processes["annotation"]
# Iterate through each project
for project in projects:
if not projects[project]["output"]:
working_dir = default_working_dir
else:
working_dir = projects[project]["output"][0]
print (project)
for process in processToBeRestarted:
print (process)
deletedProcess = os.path.join(working_dir, project, "process", "FindSV", process)
# If the entire step is to be restarted,
# delete the folder containing the status files.
if os.path.exists(deletedProcess) and not restartStatusFiles:
shutil.rmtree(deletedProcess)
# if a certain statusfile is specified, restart only that file
elif restartStatusFiles:
for files in restartStatusFiles:
deletedStatusFile = os.path.join(deletedProcess, files)
if os.path.exists(deletedStatusFile):
os.remove(deletedStatusFile)
def main(args):
programDirectory = os.path.dirname(os.path.abspath(__file__))
#read the project file
projects = {}
for file in os.listdir(os.path.join(programDirectory,"projects")):
if file.endswith(".txt") and not file.endswith("example.txt"):
with open(os.path.join(programDirectory,"projects" ,file)) as ongoing_fd:
projectID=file.split("/")[-1]
projectID=file.replace(".txt","")
#the user has selected a project manually, and it is not this one
#then there is really nothing to do.
if not (args.project and (args.project != projectID)):
projects[projectID]={};
for line in ongoing_fd:
try:
if line[0] != "#":
info=line.strip();
info = info.split("\t")
projects[projectID][info[0]]=info[1:]
except:
#the pipeline should not crash if the user adds some newlines etc to the project file
pass
# Read the config file
(working_dir, available_tools, account, exclude,modules,recursive) = readConfigFile.readConfigFile(programDirectory)
path_to_bam=""
default_working_dir=working_dir
for project in projects:
#initiate the project parameters based on the project dictionary
project_path = projects[project]["bam"]
projectName = project
#set the output,genmod and frequency db path
if not projects[project]["output"]:
working_dir = default_working_dir
else:
working_dir= projects[project]["output"][0]
if not projects[project]["genmod"]:
genmod_file = os.path.join(programDirectory,"genmod")
else:
genmod_file=projects[project]["genmod"][0]
if not projects[project]["db"]:
frequency_db=os.path.join(working_dir, project,"FindSV","database")
else:
frequency_db=projects[project]["db"][0]
processFilesPath = os.path.join(working_dir, project,"process")
#create a directory to keep track of the analysed files
if not (os.path.exists(processFilesPath)):
os.makedirs(processFilesPath)
#initate the processFiles
processFiles = initiateProcessFile(available_tools, processFilesPath)
#search for the projects bam files
bamfiles=detect_bam_files(project_path, projectName,path_to_bam,recursive)
#function used to find variants
processFiles= calling.variantCalling(
programDirectory, project_path, projectName, working_dir,
path_to_bam, available_tools, account, modules,bamfiles, exclude, processFiles,
processFilesPath)
#combine the results o the variant calling
processFiles = combine.combine(programDirectory, processFiles,
processFilesPath, account,bamfiles)
#a function used to build databases from vcf files
processFiles = database.buildDatabase(programDirectory, processFiles,
processFilesPath, account)
# Function that filters the variant files and finds genomic features of
# the variants
processFiles = filter.applyFilter(programDirectory, processFiles,
processFilesPath, account,frequency_db)
#function used to annotate the samples
processFiles = annotation.annotation(programDirectory, processFiles,
processFilesPath, account,genmod_file)
#the funciton used for cleaning the vcf file, this is the final step of the pipeline
processFiles = cleaning.cleaning(programDirectory, processFiles,
processFilesPath, account)
return
