def plotSV(svDF, refDF, uniprotPath, args):
if args.verbose:
logging.info(
"iAnnotateSV: Will now try to plot Each Structural Variants")
upDF = None
if (os.path.isfile(uniprotPath)):
upDF = hp.ReadFile(uniprotPath)
else:
if args.verbose:
logging.fatal(
"iAnnotateSV: %s file does not exist!!, Please use it to plot structural variants",
uniprotPath)
sys.exit()
vsv.VisualizeSV(svDF, refDF, upDF, args)
portTalkingTo = helper.namesAndPorts.get('A')
# Paths to where communication files are stored
pathToAnnToChanFile = './Supplemental Text Files/Ann/Ann-_Chan.txt'
pathToAnnToJanFile = './Supplemental Text Files/Ann/Ann-_Jan.txt'
# Paths to where the resulting log files from communication will be stored
pathToAnnChanLogFile = './Supplemental Text Files/Ann/AnnChanLog.txt'
pathToAnnJanLogFile = './Supplemental Text Files/Ann/AnnJanLog.txt'
# Cleaf log files at the start of the session
helper.WriteToLogFile(pathToAnnChanLogFile, 'w', '')
helper.WriteToLogFile(pathToAnnJanLogFile, 'w', '')
# Reading communication material from the text files
contentAnnToJan = helper.ReadFile(pathToAnnToJanFile)
contentAnnToChan = helper.ReadFile(pathToAnnToChanFile)
# Set this upon keyboard interrupt to let the threads know they have to exit
exitEvent = threading.Event()
# ---------------------------------------------------------------
# This class can be instantiated to create a multithreaded server
# ---------------------------------------------------------------
class ThreadedTCPServer(ThreadingMixIn, TCPServer):
"""Handle requests in a separate thread."""
# ----------------------------------------------------
# Request handler for the server portion of the agents
# Port number for Chan + 1000
listeningport = helper.namesAndPorts.get('Chan')
# Closest router Chan will be sending msgs to
talkingport = helper.namesAndPorts.get('E')
# Communication files path
chantojan_file = './Communication Files/Chan/Chan-Jan.txt'
chantoann_file = './Communication Files/Chan/Chan-Ann.txt'
# Communication Log files
chanjanlog_file = './Communication Files/Chan/Chan-JanLog.txt'
chanannlog_file = './Communication Files/Chan/Chan-AnnLog.txt'
# Traverse communication btw agents from the text files
chantojan_comm = helper.ReadFile(chantojan_file)
chantoann_comm = helper.ReadFile(chantoann_file)
# Make sure log files are empty first
helper.WriteToLogFile(chanjanlog_file, 'w', '')
helper.WriteToLogFile(chanannlog_file, 'w', '')
# Class can be instantiated to create a multi-threaded server
class ServerThread(ThreadingMixIn, TCPServer):
"""Handle requests in a separate thread."""
# Request handler for the server portion of the agents
class RequestHandler(BaseRequestHandler):
def handle(self):
def main(command=None):
parser = argparse.ArgumentParser(
prog='iAnnotateSV.py',
description='Annotate SV based on a specific human reference',
usage='%(prog)s [options]')
parser.add_argument("-v",
"--verbose",
action="store_true",
dest="verbose",
help="make lots of noise [default]")
parser.add_argument(
"-r",
"--refFileVersion",
action="store",
dest="refVersion",
required=True,
metavar='hg19',
help="Which human reference file to be used, hg18,hg19 or hg38")
parser.add_argument("-rf",
"--refFile",
action="store",
dest="refFile",
required=False,
metavar='hg19.sv.table.txt',
help="Human reference file location to be used")
parser.add_argument("-ofp",
"--outputFilePrefix",
action="store",
dest="outFilePrefix",
required=True,
metavar='test',
help="Prefix for the output file")
parser.add_argument("-o",
"--outputDir",
action="store",
dest="outDir",
required=True,
metavar='/somedir',
help="Full Path to the output dir")
parser.add_argument(
"-i",
"--svFile",
action="store",
dest="svFilename",
required=True,
metavar='svfile.txt',
help="Location of the structural variants file to annotate")
parser.add_argument("-d",
"--distance",
action="store",
dest="distance",
default=3000,
required=False,
metavar='3000',
help="Distance used to extend the promoter region")
parser.add_argument(
"-a",
"--autoSelect",
action="store_true",
dest="autoSelect",
default=True,
help="Auto Select which transcript to be used[default]")
parser.add_argument(
"-c",
"--canonicalTranscripts",
action="store",
dest="canonicalTranscripts",
required=False,
metavar='canonicalExons.txt',
help=
"Location of canonical transcript list for each gene. Use only if you want the output for specific transcripts for each gene."
)
parser.add_argument("-p",
"--plotSV",
action="store_true",
dest="plotSV",
help="Plot the structural variant in question")
parser.add_argument(
"-u",
"--uniprotFile",
action="store",
dest="uniprot",
required=False,
metavar='uniprot.txt',
help=
"Location of UniProt list contain information for protein domains. Use only if you want to plot the structural variant"
)
parser.add_argument("-rr",
"--repeatFile",
action="store",
dest="rrFilename",
required=False,
metavar='RepeatRegionFile.tsv',
help="Location of the Repeat Region Bed File")
parser.add_argument(
"-dgv",
"--dgvFile",
action="store",
dest="dgvFilename",
required=False,
metavar='DGvFile.tsv',
help="Location of the Database of Genomic Variants Bed File")
parser.add_argument("-cc",
"--cosmicConsensusFile",
action="store",
dest="ccFilename",
required=False,
metavar='CosmicConsensus.tsv',
help="Location of the Cosmic Consensus TSV file")
parser.add_argument("-cct",
"--cosmicCountsFile",
action="store",
dest="cctFilename",
required=False,
metavar='cosmic_fusion_counts.tsv',
help="Location of the Cosmic Counts TSV file")
args = ""
if (command is None):
args = parser.parse_args()
else:
args = parser.parse_args(command.split())
# Create Logger if verbose
loggeroutput = args.outDir + "/" + args.outFilePrefix + "_iAnnotateSV.log"
logging.basicConfig(
filename=loggeroutput,
filemode='w',
format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
datefmt='%m/%d/%Y %I:%M:%S %p',
level=logging.DEBUG)
coloredlogs.install(level='DEBUG')
# Check if file for canonical transcript is given or not
if (args.canonicalTranscripts):
args.autoSelect = False
this_dir, this_filename = os.path.split(__file__)
if (args.refVersion == 'hg18' or args.refVersion == 'hg19'
or args.refVersion == 'hg38'):
if (args.refFile):
pass
else:
refFile = args.refVersion + ".sv.table.txt"
refFile = os.path.join(this_dir, "data/references", refFile)
if (args.rrFilename):
rrPath = args.rrFilename
else:
rrFilename = args.refVersion + "_repeatRegion.tsv"
rrPath = os.path.join(this_dir, "data/repeat_region", rrFilename)
if (args.dgvFilename):
dgvPath = args.dgvFilename
else:
dgvFilename = args.refVersion + "_DGv_Annotation.tsv"
dgvPath = os.path.join(this_dir,
"data/database_of_genomic_variants",
dgvFilename)
if (args.ccFilename):
ccPath = args.ccFilename
else:
ccFilename = "cancer_gene_census.tsv"
ccPath = os.path.join(this_dir, "data/cosmic", ccFilename)
if (args.cctFilename):
cctPath = args.cctFilename
else:
cctFilename = "cosmic_fusion_counts.tsv"
cctPath = os.path.join(this_dir, "data/cosmic", cctFilename)
if (args.uniprot):
uniprotPath = args.uniprot
else:
upFilename = args.refVersion + ".uniprot.spAnnot.table.txt"
uniprotPath = os.path.join(this_dir, "data/UcscUniprotdomainInfo",
upFilename)
else:
if (args.verbose):
logging.fatal(
"iAnnotateSV: Please enter correct reference file version. Values can be: hg18 or hg19 or hg38"
)
sys.exit()
(refDF) = hp.ReadFile(refFile)
NewRefDF = hp.ExtendPromoterRegion(refDF, args.distance)
svDF = hp.ReadFile(args.svFilename)
annDF = processSV(svDF, NewRefDF, args)
plotDF = annDF.copy()
# Print to TSV file
outFilePrefixPath = args.outDir + "/" + args.outFilePrefix + "_functional.txt"
annDF.to_csv(outFilePrefixPath, sep='\t', index=False)
# Add External Annotations
if args.verbose:
logging.info("iAnnotateSV: Adding External Annotations...")
makeCommandLineForAEA = "-r " + rrPath + " -d " + dgvPath + " -c " + ccPath + " -cct " + cctPath + " -s " + \
outFilePrefixPath + " -ofp " + args.outFilePrefix + "_Annotated" + " -o " + args.outDir
aea.main(makeCommandLineForAEA)
# Plot if required
if (args.plotSV):
plotSV(plotDF, NewRefDF, uniprotPath, args)
if (args.verbose):
logging.info("iAnnotateSV: Finished Running the Annotation Process!!!")
talkingport = helper.namesAndPorts.get('A')
# Communication path storage
anntochan_file = './Supplemental Text Files/Ann/Ann-Chan.txt'
anntojan_file = './Supplemental Text Files/Ann/Ann-Jan.txt'
# Log file storage
annchan_logfile = './Supplemental Text Files/Ann/Ann-ChanLog.txt'
annjan_logfile = './Supplemental Text Files/Ann/Ann-JanLog.txt'
# Clearing log files
helper.WriteToLogFile(annchan_logfile, 'w', '')
helper.WriteToLogFile(annjan_logfile, 'w', '')
# reading communication files
anntojan_comm = helper.ReadFile(anntojan_file)
anntochan_comm = helper.ReadFile(anntochan_file)
threadingEvent = threading.Event()
# multithreaded server initiation
class ServerThread(ThreadingMixIn, TCPServer):
"""Handle multiple requests separately."""
# request handler class
class RequestHandler(BaseRequestHandler):
def handle(self):
# socket connecting to client here
packetgoingin = self.request.recv(4096)
packetgoingindecoded = pickle.loads(packetgoingin)
def run(svDFA, refPath, ctPath, allctPath, upPath, verbose):
if (os.path.isfile(upPath)):
upDF = hp.ReadFile(upPath)
else:
if (verbose):
logging.critical(
"iAnnotateSV::AnnotationForKinaseDomain: Location of Uniprot Annoation file is incorrect!!!"
)
sys.exit(1)
if (os.path.isfile(ctPath)):
ctDF = hp.ReadFile(ctPath)
else:
if (verbose):
logging.warn(
"iAnnotateSV::AnnotationForKinaseDomain: Location of assay specific canonical transcript file is incorrect!!!"
)
ctDF = pd.DataFrame()
if (os.path.isfile(allctPath)):
allctDF = hp.ReadFile(allctPath)
else:
if (verbose):
logging.critical(
"iAnnotateSV::AnnotationForKinaseDomain: Location of all canonical transcript file is incorrect!!!"
)
sys.exit(1)
if (os.path.isfile(refPath)):
refDF = hp.ReadFile(refPath)
refDF.columns = refDF.columns.str.replace('#', '')
else:
if (verbose):
logging.critical(
"iAnnotateSV::AnnotationForKinaseDomain: Location of reference based annotation file is incorrect!!!"
)
sys.exit(1)
svDF = svDFA.copy()
svDF.insert(loc=9, column='kinase_domain1', value=None)
svDF.insert(loc=13, column='kinase_domain2', value=None)
#svDF["kinase_domain1"] = None
#svDF["kinase_domain2"] = None
for count, row in svDFA.iterrows():
# print row
if (verbose):
logging.info(
"iAnnotateSV::AnnotateForKinaseDomain: Checking Entry %d in Uniprot data",
count)
chr1 = str(row.loc['chr1'])
chr2 = str(row.loc['chr2'])
if (chr1.startswith('chr')):
chr1 = chr1
else:
chr1 = "chr" + chr1
if (chr2.startswith('chr')):
chr2 = chr2
else:
chr2 = "chr" + chr2
pos1 = int(row.loc['pos1'])
pos2 = int(row.loc['pos2'])
gene1 = str(row.loc['gene1'])
gene2 = str(row.loc['gene2'])
site1 = str(row.loc['site1'])
site2 = str(row.loc['site2'])
try:
transcript1 = ctDF.Transcripts[ctDF.Gene[ctDF.Gene ==
gene1].index.tolist()[0]]
except IndexError:
try:
transcript1 = allctDF.Transcripts[allctDF.Gene[
allctDF.Gene == gene1].index.tolist()[0]]
except IndexError:
transcript1 = None
try:
transcript2 = ctDF.Transcripts[ctDF.Gene[ctDF.Gene ==
gene2].index.tolist()[0]]
except IndexError:
try:
transcript2 = allctDF.Transcripts[allctDF.Gene[
allctDF.Gene == gene2].index.tolist()[0]]
except IndexError:
transcript2 = None
fusion = str(row.loc['fusion'])
kanno1 = None
kanno2 = None
if (fusion != "-"):
# First Gene +, Second Gene -
fusionevent = re.search(r'\{(.*)\}', fusion)
if (fusionevent):
eventType = fusionevent.group(1)
if (":" in eventType):
# print fusion, fusionevent, eventType
(egene1, egene2) = (str(eventType)).split(":")
if (transcript1):
kanno1 = getKinaseInfo(chr1, pos1, gene1, egene1,
egene2, transcript1, refDF,
upDF)
else:
kanno1 = None
if (transcript2):
kanno2 = getKinaseInfo(chr2, pos2, gene2, egene1,
egene2, transcript2, refDF,
upDF)
else:
kanno2 = None
else:
kanno1 = None
kanno2 = None
else:
kanno1 = None
kanno2 = None
svDF.loc[count, 'kinase_domain1'] = kanno1
svDF.loc[count, 'kinase_domain2'] = kanno2
return (svDF)
# Communication path storage
jantochan_file = './Supplemental Text Files/Jan/Jan-Chan.txt'
jantoann_file = './Supplemental Text Files/Jan/Jan-Ann.txt'
# Log file storage
janchan_logfile = './Supplemental Text Files/Jan/Jan-ChanLog.txt'
janann_logfile = './Supplemental Text Files/Jan/Jan-AnnLog.txt'
janairforce_logfile = './Supplemental Text Files/Jan/Jan-AirForceLog.txt'
# Clearing log files
helper.WriteToLogFile(janchan_logfile, 'w', '')
helper.WriteToLogFile(janann_logfile, 'w', '')
helper.WriteToLogFile(janairforce_logfile, 'w', '')
# reading communication files.
jantochan_comm = helper.ReadFile(jantochan_file)
jantoann_comm = helper.ReadFile(jantoann_file)
threadingEvent = threading.Event()
# multithreaded server initiation
class ServerThread(ThreadingMixIn, TCPServer):
"""Handle requests in a separate thread."""
#request handler class
class RequestHandler(BaseRequestHandler):
def handle(self):
# socket connecting to client here.
