import MySQLdb as mdb
import csv
import sys
import smModule.misc as misc
with open("config.txt") as c:
config = misc.readConfig(c.readlines())
def flatl(l):
"""
Flattening lists made easy!
Or unpacking tuples made easy!
Try:
a = ['a','b',[1,2,3,4]]
print flatl(a)
"""
return([item for subl in l for item in subl])
def merge_intv(intervals, distance = 6):
"""
An algorithm to sort tuples with (start, end) coordinates
the last element is compared with the upper element and a new one is generated
on the fly in case the coordinates are adjacent to each other
Default argument for distance is 6, can be modified by providing a dist argument
"""
sorted_by_lower_bound = sorted(intervals, key=lambda tup: tup[0])
merged = []
global lower
action="store_true",
default=False,
help="This command uses non subsetted tables")
parser.add_argument(
"--cluster_and_visualize",
"-cv",
dest="cluster_and_visualize",
action="store_true",
default=False,
help=
"If you only want to rerun clustering and visualization, choose this option"
)
args = parser.parse_args()
with open("config.txt") as c:
config = readConfig(c.readlines())
print("Queries to format smurf databases")
if args.otherBlast:
print("%s -in smurf.fasta -dbtype prot" % config['makeblastdbPath'])
else:
print("%s -i smurf.fasta" % config['formatDbPath'])
########
# LOADING ORGS
filename = args.filename
biblastBaseTable = args.bibase
smurfBidirHitsName = args.biFinal
testLogName = args.logFile