def readTransfer(file, flag='symbol', head=1):
if flag == 'symbol':
symbolDict = {}
flag = 1
elif flag == 'locus':
locusDict = {}
flag = 2
else:
print >> sys.stderr, "Wrong flag, should be 'symbol' or 'locus'"
sys.exit(1)
#---------------------------------------------
for line in open(file):
if head:
head -= 1
continue
#-------------------------
line = line.rstrip()
(locus, symbol, name) = line.split('\t')
name = name.upper()
if flag == 1:
symbol = symbol.upper()
if pattern.match(symbol):
#print >>sys.stderr, symbol, name
#assert symbol == name
if symbol != name:
print >> sys.stderr, symbol, name
name = symbol
if flag == 1:
#There are duplicate symbols, before use list to save
#names, later change to set.
if symbol not in symbolDict:
symbolDict[symbol] = set()
symbolDict[symbol].add(name)
elif flag == 2:
#Do not know if there are duplicate locus
if locus not in locusDict:
locusDict[locus] = set()
locusDict[locus].add(name)
#-------------------------------------------
#------------End reading------------------
if flag == 1:
if 0:
ctTEST.ct_rdict(symbolDict)
sys.exit()
return symbolDict
elif flag == 2:
return locusDict
def readTransfer(file, flag = 'symbol', head = 1):
if flag == 'symbol':
symbolDict = {}
flag = 1
elif flag == 'locus':
locusDict = {}
flag = 2
else:
print >>sys.stderr, "Wrong flag, should be 'symbol' or 'locus'"
sys.exit(1)
#---------------------------------------------
for line in open(file):
if head:
head -= 1
continue
#-------------------------
line = line.rstrip()
(locus, symbol, name) = line.split('\t')
name = name.upper()
if flag == 1:
symbol = symbol.upper()
if pattern.match(symbol):
#print >>sys.stderr, symbol, name
#assert symbol == name
if symbol != name:
print >>sys.stderr, symbol, name
name = symbol
if flag == 1:
#There are duplicate symbols, before use list to save
#names, later change to set.
if symbol not in symbolDict:
symbolDict[symbol] = set()
symbolDict[symbol].add(name)
elif flag == 2:
#Do not know if there are duplicate locus
if locus not in locusDict:
locusDict[locus] = set()
locusDict[locus].add(name)
#-------------------------------------------
#------------End reading------------------
if flag == 1:
if 0:
ctTEST.ct_rdict(symbolDict)
sys.exit()
return symbolDict
elif flag == 2:
return locusDict
def readInterpro(interprofile, locusL):
"""
pfamDict = {'PF01209':['AT5G57290.3',], 'Ubie':[AT5G57290.3]}
iprDict = {'IPR001813':['AT5G57290.3',], 'Ribosomal':[AT5G57290.3]}
mfDict = {'GO:0008168':[AT5G57300.2], 'methy':[AT5G57300.2]}
bpDict = {'GO:0008168':[AT5G57300.2], 'methy':[AT5G57300.2]}
ccDict = {'GO:0008168':[AT5G57300.2], 'methy':[AT5G57300.2]}
"""
pfamDict = {}
iprDict = {}
mfDict = {}
bpDict = {}
ccDict = {}
# pfamsymkeySet = set()
# pfamdspkeySet = set()
# iprsymkeySet = set()
# iprdspkeySet = set()
for line in open(interprofile):
lineL = line.rstrip().split("\t")
locus = lineL[0]
if locus not in locusL:
continue
pfamsym = lineL[4]
pfamdsp = lineL[5]
# if 1:
# print '%s\t%s' % (pfamsym, pfamdsp)
# pfamsymkeySet.add(pfamsym)
# pfamdspkeySet.add(pfamdsp)
add2dict(pfamDict, pfamsym, pfamdsp, locus)
iprsym = lineL[11]
iprdsp = lineL[12]
# iprsymkeySet.add(iprsym)
# iprdspkeySet.add(iprdsp)
add2dict(iprDict, iprsym, iprdsp, locus)
if len(lineL) == 14:
addgo(lineL[13], bpDict, ccDict, mfDict, locus)
# ---End go extract all----------------------------
# ----end read file
# assert len(pfamsymkeySet) == len(pfamdspkeySet)
# assert len(iprsymkeySet) == len(iprdspkeySet)
if TESTdict:
ct_rdict(pfamDict)
print >> sys.stderr, "Test finished"
sys.exit(1)
return (pfamDict, iprDict, bpDict, ccDict, mfDict)
def readInterpro(interprofile, locusL):
'''
pfamDict = {'PF01209':['AT5G57290.3',], 'Ubie':[AT5G57290.3]}
iprDict = {'IPR001813':['AT5G57290.3',], 'Ribosomal':[AT5G57290.3]}
mfDict = {'GO:0008168':[AT5G57300.2], 'methy':[AT5G57300.2]}
bpDict = {'GO:0008168':[AT5G57300.2], 'methy':[AT5G57300.2]}
ccDict = {'GO:0008168':[AT5G57300.2], 'methy':[AT5G57300.2]}
'''
pfamDict = {}
iprDict = {}
mfDict = {}
bpDict = {}
ccDict = {}
#pfamsymkeySet = set()
#pfamdspkeySet = set()
#iprsymkeySet = set()
#iprdspkeySet = set()
for line in open(interprofile):
lineL = line.rstrip().split('\t')
locus = lineL[0]
if locus not in locusL:
continue
pfamsym = lineL[4]
pfamdsp = lineL[5]
#if 1:
# print '%s\t%s' % (pfamsym, pfamdsp)
#pfamsymkeySet.add(pfamsym)
#pfamdspkeySet.add(pfamdsp)
add2dict(pfamDict, pfamsym, pfamdsp, locus)
iprsym = lineL[11]
iprdsp = lineL[12]
#iprsymkeySet.add(iprsym)
#iprdspkeySet.add(iprdsp)
add2dict(iprDict, iprsym, iprdsp, locus)
if len(lineL) == 14:
addgo(lineL[13], bpDict, ccDict, mfDict, locus)
#---End go extract all----------------------------
#----end read file
#assert len(pfamsymkeySet) == len(pfamdspkeySet)
#assert len(iprsymkeySet) == len(iprdspkeySet)
if TESTdict:
ct_rdict(pfamDict)
print >>sys.stderr, "Test finished"
sys.exit(1)
return (pfamDict, iprDict, bpDict, ccDict, mfDict)