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()
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()