def ingame_menu():
"""The menu that appears after the main menu/the first menu"""
# While loop for continous play
while True:
# Tells user that typing q goes to the main menu
print('type q to go back to the main menu')
# Asks for user input
menu = input('type map/inventory/characters: ')
# Makes all the user input into lower case
menu = menu.lower()
# Checks to see if user typed inventory
if menu == 'inventory':
# Tells user to type in certain commands to access further menus
print('type [weapon], [fishing rod], [heal]')
# Runs the inventory function
inv.inventory()
# Checks to see if user typed location
elif menu == 'map':
# Runs the location function
loc.location()
elif menu == 'characters':
ch.all_characters()
# Checks to see if user typed in q
elif menu == 'q':
# Goes to main menu
break
# Checks to see if anything else was typed in
else:
# Tells user that was an invalid selection
print('invalid select again')
def translocation(chr1, pos1, chr2, pos2, ct):
secondStrand = "+"
firstExtendRight = False
secondExtendRight = True
if ct is None or ct == '3to5':
pass
elif ct == '5to3':
firstExtendRight = True; secondExtendRight = False
elif ct == '5to5':
firstExtendRight = True; secondExtendRight = True; secondStrand = '-'
elif ct == '3to3':
firstExtendRight =False; secondExtendRight =False; secondStrand = '-'
return ( loc.location(chr1, pos1, "+", firstExtendRight),
loc.location(chr2, pos2, secondStrand, secondExtendRight) )
def translocation(chr1, pos1, chr2, pos2, ct):
secondStrand = "+"
firstExtendRight = False
secondExtendRight = True
if ct is None or ct == '3to5':
pass
elif ct == '5to3':
firstExtendRight = True
secondExtendRight = False
elif ct == '5to5':
firstExtendRight = True
secondExtendRight = True
secondStrand = '-'
elif ct == '3to3':
firstExtendRight = False
secondExtendRight = False
secondStrand = '-'
return (loc.location(chr1, pos1, "+", firstExtendRight),
loc.location(chr2, pos2, secondStrand, secondExtendRight))
def breakpointsFromRecord(record):
"""Returns a list of pair(s) of breakpoints corresponding to the record."""
global __symbolicRE__
global __bpRE__
global __looseendRE__
chr1, pos1 = stdchrom(record.CHROM), int(record.POS)
first = loc.location(chr1, pos1)
if record.ALT is None:
return [(first, loc.location(None, 0, "+", True))]
setupREs()
ref = str(record.REF)
bkptPairs = []
for alt in record.ALT:
if alt is None:
altstr = "."
else:
altstr = str(alt)
# get all available information from the record
chr2, pos2, ct, svtype, svlen = otherPosnSymbolic(record.INFO)
# defaults
if chr2 is None:
chr2 = chr1
# look for symbolic SVTYPE information in the alt field (eg, <DEL>)
resultSym = re.match(__symbolicRE__, altstr)
if resultSym:
svtype = resultSym.group(1)
# explicit BP - look for chr2 and CT information from the alt field
# (eg, N[chr2:123123[)
resultBP = re.match(__bpRE__, altstr)
if resultBP:
ct, chr2, pos2, indellen = ctAndLocFromBkpt(
str(record.REF), resultBP.group(1), resultBP.group(2),
resultBP.group(3), resultBP.group(4), resultBP.group(5))
if svlen is None:
svlen = indellen
# looseend; no paired BP
resultLE = __looseendRE__.search(str(record.FILTER))
if altstr == ref + "." or resultLE:
chr2 = None
pos2 = 0
if ct is None:
ct = '5to3'
if altstr == "." + ref:
chr2 = None
pos2 = 0
if ct is None:
ct = '3to5'
# if nothing else, treat as an indel
if not svtype and not resultBP and not resultLE and not resultSym:
reflen = len(ref)
if pos2 is None:
pos2 = pos1 + reflen
if svlen is None:
svlen = len(altstr) - reflen
if svtype is None:
if svlen > 0:
svtype = 'INS'
else:
svtype = 'DEL'
if svtype == "INV":
assert chr1 == chr2
bkptPairs.append(translocation(chr1, pos1, chr1, pos2 - 1, '3to3'))
bkptPairs.append(translocation(chr1, pos1 + 1, chr1, pos2, '5to5'))
elif svtype in ["DUP:TANDEM", "DUP"]:
if chr2 is None:
chr2 = chr1
if ct is None or ct == "5to3" or ct == "3to5":
if pos1 > pos2:
pos1, pos2 = pos2, pos1
bkptPairs.append(translocation(chr1, pos1, chr2, pos2, "5to3"))
else:
bkptPairs.append(translocation(chr1, pos1, chr2, pos2, ct))
elif svtype in ["INS", "INS:ME:L1"]:
assert chr1 == chr2
bkptPairs.append((first, loc.location(chr1, pos1 + 1, "+", True)))
elif svtype in ["DEL:ME:ALU", "DEL"]:
assert chr1 == chr2
bkptPairs.append(
translocation(chr1, min(pos1, pos2), chr1, max(pos1, pos2),
'3to5'))
else:
# translocation is the default
if ct is None:
ct = "3to5"
if (svtype is not None) and (not svtype in ["TRA", "BND"]):
print("Got unknown record of type",
svtype,
altstr,
str(record),
file=sys.stderr)
print("Hoping for best", file=sys.stderr)
bkptPairs.append(translocation(chr1, pos1, chr2, pos2, ct))
orderedPairs = [orderBreakpoints(bp1, bp2) for bp1, bp2 in bkptPairs]
return orderedPairs
def breakpointsFromRecord(record):
"""Returns a list of pair(s) of breakpoints corresponding to the record."""
global __symbolicRE__
global __bpRE__
global __looseendRE__
chr1, pos1 = stdchrom(record.CHROM), int(record.POS)
first = loc.location(chr1, pos1)
if record.ALT is None:
return [(first, loc.location(None,0,"+",True))]
setupREs()
ref = str(record.REF)
bkptPairs = []
for alt in record.ALT:
if alt is None:
altstr = "."
else:
altstr = str(alt)
# get all available information from the record
chr2, pos2, ct, svtype, svlen = otherPosnSymbolic(record.INFO)
# defaults
if chr2 is None:
chr2 = chr1
# look for symbolic SVTYPE information in the alt field (eg, <DEL>)
resultSym = re.match(__symbolicRE__, altstr)
if resultSym:
svtype = resultSym.group(1)
# explicit BP - look for chr2 and CT information from the alt field
# (eg, N[chr2:123123[)
resultBP = re.match(__bpRE__, altstr)
if resultBP:
ct, chr2, pos2, indellen = ctAndLocFromBkpt(str(record.REF), resultBP.group(1),
resultBP.group(2), resultBP.group(3), resultBP.group(4),
resultBP.group(5))
if svlen is None:
svlen = indellen
# looseend; no paired BP
resultLE = __looseendRE__.search(str(record.FILTER))
if altstr == ref+"." or resultLE:
chr2 = None; pos2 = 0
if ct is None:
ct = '5to3'
if altstr == "."+ref:
chr2 = None; pos2 = 0
if ct is None:
ct = '3to5'
# if nothing else, treat as an indel
if not svtype and not resultBP and not resultLE and not resultSym:
reflen = len(ref)
if pos2 is None:
pos2 = pos1 + reflen
if svlen is None:
svlen = len(altstr) - reflen
if svtype is None:
if svlen > 0:
svtype = 'INS'
else:
svtype = 'DEL'
if svtype == "INV":
assert chr1 == chr2
bkptPairs.append( translocation(chr1, pos1, chr1, pos2-1, '3to3') )
bkptPairs.append( translocation(chr1, pos1+1, chr1, pos2, '5to5') )
elif svtype in ["DUP:TANDEM","DUP"]:
if chr2 is None:
chr2 = chr1
if ct is None or ct=="5to3" or ct=="3to5":
if pos1 > pos2:
pos1, pos2 = pos2, pos1
bkptPairs.append( translocation(chr1, pos1, chr2, pos2, "5to3") )
else:
bkptPairs.append( translocation(chr1, pos1, chr2, pos2, ct) )
elif svtype in ["INS","INS:ME:L1"]:
assert chr1 == chr2
bkptPairs.append((first, loc.location(chr1, pos1+1, "+", True)))
elif svtype in ["DEL:ME:ALU","DEL"]:
assert chr1 == chr2
bkptPairs.append( translocation(chr1, min(pos1,pos2), chr1, max(pos1,pos2), '3to5') )
else:
# translocation is the default
if ct is None:
ct = "3to5"
if (svtype is not None) and (not svtype in ["TRA","BND"]):
print("Got unknown record of type", svtype, altstr, str(record), file=sys.stderr)
print("Hoping for best",file=sys.stderr)
bkptPairs.append( translocation(chr1, pos1, chr2, pos2, ct) )
orderedPairs = [orderBreakpoints(bp1,bp2) for bp1,bp2 in bkptPairs]
return orderedPairs