def main():
print >> sys.stderr, "Print the result to current directory"
lenS = len(sys.argv)
if lenS != 3 and lenS != 2:
print >> sys.stderr, 'Using python %s seqfile(for.c) [locus](optional)' % sys.argv[
0]
sys.exit(0)
#--------------------------------
seqDict = {}
ctIO.readseq(sys.argv[1], seqDict)
locusDict = {}
if lenS == 2:
locusL = seqDict.keys()
locusL.sort()
elif lenS == 3:
locusL = [line.strip() for line in open(sys.argv[2])]
for line in locusL:
line = line.strip()
dot = line.find('.')
locus = line[:dot]
after = line[dot:]
if locus in locusDict:
locusDict[locus].append(after)
else:
locusDict[locus] = [after]
#--------------------------------
fhl = open('locusHasIsoforms', 'w')
for locus, afterL in locusDict.items():
if len(afterL) < 2:
continue
filename = locus + '.fa'
fh = open(filename, 'w')
for after in afterL:
newLoc = locus + after
print >> fhl, newLoc
print >> fh, '>%s' % newLoc
print >> fh, seqDict[newLoc]
fh.close()
cmd = 't_coffee ' + filename
os.system(cmd)
#---------------------------
fhl.close()
def main():
print >>sys.stderr, "Print the result to current directory"
lenS = len(sys.argv)
if lenS != 3 and lenS != 2:
print >>sys.stderr, 'Using python %s seqfile(for.c) [locus](optional)' % sys.argv[0]
sys.exit(0)
#--------------------------------
seqDict = {}
ctIO.readseq(sys.argv[1], seqDict)
locusDict = {}
if lenS == 2:
locusL = seqDict.keys()
locusL.sort()
elif lenS == 3:
locusL = [line.strip() for line in open(sys.argv[2])]
for line in locusL:
line = line.strip()
dot = line.find('.')
locus = line[:dot]
after = line[dot:]
if locus in locusDict:
locusDict[locus].append(after)
else:
locusDict[locus] = [after]
#--------------------------------
fhl = open('locusHasIsoforms', 'w')
for locus, afterL in locusDict.items():
if len(afterL) < 2:
continue
filename = locus+'.fa'
fh = open(filename, 'w')
for after in afterL:
newLoc = locus+after
print >>fhl, newLoc
print >>fh, '>%s' % newLoc
print >>fh, seqDict[newLoc]
fh.close()
cmd = 't_coffee ' + filename
os.system(cmd)
#---------------------------
fhl.close()
def main():
print >> sys.stderr, "Paste the mother sequene and related\
repetition together"
print >> sys.stderr, "Print the result to screen"
if len(sys.argv) < 3:
print >> sys.stderr, 'Using python %s forc repResult \
[anno] [locus] ' % sys.argv[0]
sys.exit(0)
seqDict = {}
readseq(sys.argv[1], seqDict)
#--------------------------------------------
isAnno = 0
if sys.argv[3]:
isAnno = 1
annoDict = {}
readAnno(sys.argv[3], annoDict)
#--------------------------------------------
isLoc = 0
if sys.argv[4]:
isLoc = 1
locL = [locus.strip() for locus in open(sys.argv[4])]
#--------------------------------------------
for line in open(sys.argv[2]):
if line[0] == '>':
output = 1
locus = line[1:].strip()
if isLoc and \
(locus not in locL) and \
(locus[:-2] not in locL):
output = 0
continue
#------------------------------------
print '>', locus
if isAnno and locus in annoDict:
print annoDict[locus]
if locus in seqDict:
print seqDict[locus]
else:
if output:
print line,
def main():
print >>sys.stderr, "Print the result to screen"
if len(sys.argv) != 3:
print >>sys.stderr, 'Using python %s seqforc curatedRep' % sys.argv[0]
sys.exit(0)
seqDict = {}
ctIO.readseq(sys.argv[1], seqDict)
repDict = {}
for line in open(sys.argv[2]):
if line[0] == '>':
locus = line[1:]
locus = locus.strip()
seq = seqDict[locus]
shift = 0
repDict[locus] = {}
else:
starPos = line.find('*')
if starPos != -1:
rep = line[:starPos]
rep = rep.strip()
rep = rep.replace(' ','')
repstart = seq.find(rep, shift)
if repstart == -1:
print >>sys.stderr, 'No such repetition %s'\
% rep
sys.exit(0)
shift = repstart + len(rep)
key = '*' * line.count('*')
if key not in repDict[locus]:
repDict[locus][key] = []
repDict[locus][key].append(rep+':'+str(repstart+1))
#---------id rep-------------------
#----------Not locus line-------------
#-------------End reading-----------------
for locus, sonDict in repDict.items():
if len(sonDict) > 0:
print '>%s' % locus
for value in sonDict.values():
print '#'.join(value)
else:
print >>sys.stderr, locus
def main():
print >> sys.stderr, "Print the result to screen"
if len(sys.argv) != 3:
print >> sys.stderr, 'Using python %s seqforc curatedRep' % sys.argv[0]
sys.exit(0)
seqDict = {}
ctIO.readseq(sys.argv[1], seqDict)
repDict = {}
for line in open(sys.argv[2]):
if line[0] == '>':
locus = line[1:]
locus = locus.strip()
seq = seqDict[locus]
shift = 0
repDict[locus] = {}
else:
starPos = line.find('*')
if starPos != -1:
rep = line[:starPos]
rep = rep.strip()
rep = rep.replace(' ', '')
repstart = seq.find(rep, shift)
if repstart == -1:
print >>sys.stderr, 'No such repetition %s'\
% rep
sys.exit(0)
shift = repstart + len(rep)
key = '*' * line.count('*')
if key not in repDict[locus]:
repDict[locus][key] = []
repDict[locus][key].append(rep + ':' + str(repstart + 1))
#---------id rep-------------------
#----------Not locus line-------------
#-------------End reading-----------------
for locus, sonDict in repDict.items():
if len(sonDict) > 0:
print '>%s' % locus
for value in sonDict.values():
print '#'.join(value)
else:
print >> sys.stderr, locus
def main():
print >>sys.stderr, "Paste the mother sequene and related\
repetition together"
print >>sys.stderr, "Print the result to screen"
if len(sys.argv) < 3:
print >>sys.stderr, 'Using python %s forc repResult \
[anno] [locus] ' % sys.argv[0]
sys.exit(0)
seqDict = {}
readseq(sys.argv[1], seqDict)
#--------------------------------------------
isAnno = 0
if sys.argv[3]:
isAnno = 1
annoDict = {}
readAnno(sys.argv[3], annoDict)
#--------------------------------------------
isLoc = 0
if sys.argv[4]:
isLoc = 1
locL = [locus.strip() for locus in open(sys.argv[4])]
#--------------------------------------------
for line in open(sys.argv[2]):
if line[0] == '>':
output = 1
locus = line[1:].strip()
if isLoc and \
(locus not in locL) and \
(locus[:-2] not in locL):
output = 0
continue
#------------------------------------
print '>', locus
if isAnno and locus in annoDict:
print annoDict[locus]
if locus in seqDict:
print seqDict[locus]
else:
if output:
print line,
def main():
print >>sys.stderr, "Paste the mother sequene and related\
repetition together"
print >>sys.stderr, "Print the result to screen"
if len(sys.argv) < 3:
print >>sys.stderr, 'Using python %s forc repResult \
[anno] [locus] ' % sys.argv[0]
sys.exit(0)
tair = \
"http://www.arabidopsis.org/servlets/TairObject?name=&type=locus"
seqDict = {}
readseq(sys.argv[1], seqDict)
#--------------------------------------------
isAnno = 0
if len(sys.argv) > 3:
if sys.argv[3]:
isAnno = 1
annoDict = {}
readAnnoNew(sys.argv[3], annoDict)
#--------------------------------------------
isLoc = 0
if len(sys.argv) > 4:
if sys.argv[4]:
isLoc = 1
locL = [locus.strip() for locus in open(sys.argv[4])]
#--------------------------------------------
repDict = {}
'''
repDict =
{
AT1G62760:
[
{(25, 31): 'SSLSPSS', (51,57): 'SSLSPSS'},
{(52, 60): 'SLSPSSPPP',},
]
}
'''
readRep(sys.argv[2], repDict)
#-------------------------------------------
repDictKeyL = repDict.keys()
repDictKeyL.sort()
for locus in repDictKeyL:
if isLoc and (locus not in locL) and \
(locus[:-2] not in locL):
continue
#------------------------------------
print '>', locus
locusSub = "name=" + locus[:-2]
print tair.replace("name=", locusSub)
if isAnno and locus in annoDict:
print annoDict[locus].replace('\\\\', '\n')
#if locus in seqDict:
# print seqDict[locus]
seq = seqDict[locus] #this substitute the last one for we
#know it has this key, if not, wrong
locusRepL = repDict[locus]
repoutput = []
for repitemDIct in locusRepL:
grep = ''
posKey = repitemDIct.keys()
posKey.sort()
for pos in posKey:
rep = repitemDIct[pos]
grep += ':'.join([rep, str(pos[0]), str(pos[1])])
reps = '*'+rep+'*'
seq = seq.replace(rep, reps)
repoutput.append(grep)
print seq
print '\n'.join(repoutput)
def main():
(options, args) = cmdpara(sys.argv)
if options.sort:
print 'sort'
sys.exit(1)
else:
print 'no sort'
sys.exit(1)
print >> sys.stderr, "*******Print the result to screen.*******"
#-------------------macro-------------------------------------
isRep = 0
isLoc = 0
#-------------------------------------------------------------
if options.seqfile != None:
seqdict = {}
ctIO.readseq(options.seqfile, seqdict)
if options.seqrepfile != None:
seqdict = {}
repdict = {}
ctIO.readseqrep(options.seqrepfile, seqdict, repdict)
isRep = 1
if options.repfile != None:
repdict = {}
ctIO.readRep(options.repfile, repdict)
isRep = 1
if options.locusfile != None:
locusList = [line.strip() for line in open(options.locusfile)]
isLoc = 1
if not isLoc:
locusList = repdict.keys() if isRep else seqdict.keys()
locusList.sort()
if isRep or isLoc:
annodict = {}
ctIO.readAnno(options.anno, annodict, 1, locusList)
interproDict = {}
ctIO.readInterpro(options.interpro, interproDict, locusList)
#print locusList
#print repdict.keys()
#print repdict
#print isRep
#sys.exit(1)
#----------------------------------------------------------------
latexHead()
latexExplain()
#---------------------------------------------------------------
for id in locusList:
if id not in seqdict:
print >> sys.stderr, "Unknown locus %s" % id
else:
hasInterpro = 0
seq = list(seqdict[id])
#-------------get newDict--------------------------------
newDict = {}
if id in interproDict:
hasInterpro = 1
domainDespList = []
domainPosL = interproDict[id].keys()
getnewDictDomain(interproDict[id], domainDespList, newDict)
#------------------------------------------------
if isRep:
repDespList = []
repdictSonL = repdict[id]
num = len(repdictSonL)
if not hasInterpro:
domainPosL = []
getnewDictRep(repdictSonL, domainPosL, repDespList, newDict)
getnewDictRepDesp(id, num, repDespList)
#----------------get newDict---------------------------
modifySeq(seq, newDict)
#---------------------------------------------------------
shortAnno = ''
annos = annodict[id].replace('_', r'\_')
annos = annos.replace('%', r'\%')
annos = annos.replace('~', r'\~')
annos = annos.replace('&', r'\&')
firstBr = annos.find('[')
if firstBr != -1:
shortAnno = annos[:firstBr]
print ''.join((r'\section{', id, ' ', shortAnno, '}'))
annos = r'\tair{' + id[:-2] + '} ' + annos
print r'\anno{', annos, '}'
print r'''
\noindent\begin{minipage}{\textwidth}
\noindent\rule{\textwidth}{2pt}
\DNA!'''
#--without annotation
seq = ''.join(seq)
print seq
print r'''!
\end{minipage}
'''
#------------------------------------------------
print
print '.' * 100
print
#---------------Rep------------------------------
if isRep:
for repSeq in repDespList:
print repSeq
print
#-------------Domain desp----------------------
if hasInterpro:
print '.' * 100
print
for domainDesp in domainDespList:
print domainDesp
print
print r'\clearpage'
print
#----------------End of else ---one locus-------------
#----------------END of for ---all locus------------------
latexTail()
def main():
(options, args) = cmdpara(sys.argv)
print >> sys.stderr, "*******Print the result to screen.*******"
# -------------------macro-------------------------------------
isRep = 0
isLoc = 0
# -------------------------------------------------------------
if options.seqfile != None:
seqdict = {}
ctIO.readseq(options.seqfile, seqdict)
if options.seqrepfile != None:
seqdict = {}
repdict = {}
ctIO.readseqrep(options.seqrepfile, seqdict, repdict)
isRep = 1
if options.repfile != None:
repdict = {}
ctIO.readRep(options.repfile, repdict)
isRep = 1
if options.locusfile != None:
locusList = [line.strip() for line in open(options.locusfile)]
isLoc = 1
if not isLoc:
locusList = repdict.keys() if isRep else seqdict.keys()
if isRep or isLoc:
annodict = {}
ctIO.readAnno(options.anno, annodict, 1, locusList)
interproDict = {}
ctIO.readInterpro(options.interpro, interproDict, locusList)
# print locusList
# print repdict.keys()
# print repdict
# print isRep
# sys.exit(1)
# ----------------------------------------------------------------
latexHead()
latexExplain()
# ---------------------------------------------------------------
for id in locusList:
if id not in seqdict:
print >> sys.stderr, "Unknown locus %s" % id
else:
hasInterpro = 0
seq = list(seqdict[id])
# -------------get newDict--------------------------------
newDict = {}
if id in interproDict:
hasInterpro = 1
domainDespList = []
domainPosL = interproDict[id].keys()
getnewDictDomain(interproDict[id], domainDespList, newDict)
# ------------------------------------------------
if isRep:
repDespList = []
repdictSonL = repdict[id]
num = len(repdictSonL)
if not hasInterpro:
domainPosL = []
getnewDictRep(repdictSonL, domainPosL, repDespList, newDict)
getnewDictRepDesp(id, num, repDespList)
# ----------------get newDict---------------------------
modifySeq(seq, newDict)
# ---------------------------------------------------------
print "".join((r"\section{", id, "}"))
annos = annodict[id].replace("_", r"\_")
annos = annos.replace("%", r"\%")
annos = annos.replace("~", r"\~")
annos = annos.replace("&", r"\&")
annos = r"\tair{" + id[:-2] + "} " + annos
print r"\anno{", annos, "}"
print r"""
\noindent\begin{minipage}{\textwidth}
\noindent\rule{\textwidth}{2pt}
\DNA!"""
# --without annotation
seq = "".join(seq)
print seq
print r"""!
\end{minipage}
"""
# ------------------------------------------------
print
print "." * 100
print
# ---------------Rep------------------------------
if isRep:
for repSeq in repDespList:
print repSeq
print
# -------------Domain desp----------------------
if hasInterpro:
print "." * 100
print
for domainDesp in domainDespList:
print domainDesp
print
print r"\clearpage"
print
# ----------------End of else ---one locus-------------
# ----------------END of for ---all locus------------------
latexTail()
def main():
(options, args) = cmdpara(sys.argv)
if options.sort:
print 'sort'
sys.exit(1)
else:
print 'no sort'
sys.exit(1)
print >>sys.stderr, "*******Print the result to screen.*******"
#-------------------macro-------------------------------------
isRep = 0
isLoc = 0
#-------------------------------------------------------------
if options.seqfile != None:
seqdict = {}
ctIO.readseq(options.seqfile, seqdict)
if options.seqrepfile != None:
seqdict = {}
repdict = {}
ctIO.readseqrep(options.seqrepfile, seqdict, repdict)
isRep = 1
if options.repfile != None:
repdict = {}
ctIO.readRep(options.repfile, repdict)
isRep = 1
if options.locusfile != None:
locusList = [line.strip() for line in open(options.locusfile)]
isLoc = 1
if not isLoc:
locusList = repdict.keys() if isRep else seqdict.keys()
locusList.sort()
if isRep or isLoc:
annodict = {}
ctIO.readAnno(options.anno, annodict, 1, locusList)
interproDict = {}
ctIO.readInterpro(options.interpro, interproDict, locusList)
#print locusList
#print repdict.keys()
#print repdict
#print isRep
#sys.exit(1)
#----------------------------------------------------------------
latexHead()
latexExplain()
#---------------------------------------------------------------
for id in locusList:
if id not in seqdict:
print >>sys.stderr, "Unknown locus %s" % id
else:
hasInterpro = 0
seq = list(seqdict[id])
#-------------get newDict--------------------------------
newDict = {}
if id in interproDict:
hasInterpro = 1
domainDespList = []
domainPosL = interproDict[id].keys()
getnewDictDomain(interproDict[id], domainDespList,
newDict)
#------------------------------------------------
if isRep:
repDespList = []
repdictSonL = repdict[id]
num = len(repdictSonL)
if not hasInterpro:
domainPosL = []
getnewDictRep(repdictSonL, domainPosL, repDespList, newDict)
getnewDictRepDesp(id, num, repDespList)
#----------------get newDict---------------------------
modifySeq(seq, newDict)
#---------------------------------------------------------
shortAnno = ''
annos = annodict[id].replace('_', r'\_')
annos = annos.replace('%', r'\%')
annos = annos.replace('~', r'\~')
annos = annos.replace('&', r'\&')
firstBr = annos.find('[')
if firstBr != -1:
shortAnno = annos[:firstBr]
print ''.join((r'\section{', id, ' ', shortAnno, '}' ))
annos = r'\tair{' + id[:-2] + '} ' + annos
print r'\anno{', annos, '}'
print r'''
\noindent\begin{minipage}{\textwidth}
\noindent\rule{\textwidth}{2pt}
\DNA!'''
#--without annotation
seq = ''.join(seq)
print seq
print r'''!
\end{minipage}
'''
#------------------------------------------------
print
print '.' * 100
print
#---------------Rep------------------------------
if isRep:
for repSeq in repDespList:
print repSeq
print
#-------------Domain desp----------------------
if hasInterpro:
print '.' * 100
print
for domainDesp in domainDespList:
print domainDesp
print
print r'\clearpage'
print
#----------------End of else ---one locus-------------
#----------------END of for ---all locus------------------
latexTail()