def __iter__(self):
for i in self.saminfo:
yield i, self.references[i.tid]
if __name__ == "__main__":
optlist, args = getopt.getopt(sys.argv[1:], '')
optlist = dict(optlist)
if not args:
logging.error("Insufficient parameters: {0} <ms.fa.msdesc>".format(
sys.argv[0]))
sys.exit(-1)
bg = BaitDesc(open(sys.argv[1]))
samfile = pysam.Samfile("-", "r")
deal = Dealer(samfile)
dbconn = GMOD.getDBConn()
sampledone = set()
counter = 0
for i, ref in deal:
qname = i.qname.split("@")
sample = qname[0]
if sample not in sampledone:
sampledone.add(sample)
logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.DEBUG)
if __name__=="__main__":
USAGE=''' Reads a .msdesc file (MS description file) and generates a FastA file containing
all the baits according to the specified parameters'''
parser = argparse.ArgumentParser(usage=USAGE)
parser.add_argument("-i", dest="input",help="Input MS description file. [.msdesc]",required=True)
parser.add_argument("-b", dest="bottomlimit",help="Bottom limit (in bp) for the microsatellite length. [10]",default=10,type=int)
parser.add_argument("-t", dest="toplimit",help="Top limit (in bp) for the microsatellite length. [35]",default=35,type=int)
parser.add_argument("-o", dest="output",help="File output (FastaA file). If not specified [out-baits.fa] will be used",default="out-baits.fa")
args = parser.parse_args()
if args.bottomlimit>=args.toplimit: parser.error("Bottom limit cannot be higher than top limit.")
fin=open(args.input)
fout=open(args.output,"w")
try:
bd=BaitDesc(fin)
except KeyboardInterrupt as e:
print "Cancelling..."
sys.exit(-1)
bd.generatelist(args.bottomlimit,args.toplimit,fout)
fin.close()
fout.close()
logging.info( " *** [ {0} ] *** WRITTEN!".format(args.output))
"-t",
dest="toplimit",
help="Top limit (in bp) for the microsatellite length. [35]",
default=35,
type=int)
parser.add_argument(
"-o",
dest="output",
help=
"File output (FastaA file). If not specified [out-baits.fa] will be used",
default="out-baits.fa")
args = parser.parse_args()
if args.bottomlimit >= args.toplimit:
parser.error("Bottom limit cannot be higher than top limit.")
fin = open(args.input)
fout = open(args.output, "w")
try:
bd = BaitDesc(fin)
except KeyboardInterrupt as e:
print "Cancelling..."
sys.exit(-1)
bd.generatelist(args.bottomlimit, args.toplimit, fout)
fin.close()
fout.close()
logging.info(" *** [ {0} ] *** WRITTEN!".format(args.output))
self.references=saminfo.references
def __iter__(self):
for i in self.saminfo:
yield i,self.references[i.tid]
if __name__=="__main__":
optlist, args = getopt.getopt(sys.argv[1:],'')
optlist=dict(optlist)
if not args:
logging.error("Insufficient parameters: {0} <ms.fa.msdesc>".format(sys.argv[0]))
sys.exit(-1)
bg=BaitDesc(open(sys.argv[1]))
samfile = pysam.Samfile("-", "r" )
deal=Dealer(samfile)
dbconn=GMOD.getDBConn()
sampledone=set()
counter=0
for i,ref in deal:
qname=i.qname.split("@")
sample=qname[0]
if sample not in sampledone:
sampledone.add(sample)