def SelectPairaln(pairalnFile, pairlistSet, fpout): #{{{
try:
numPairToSelect = len(pairlistSet)
cntSelectedPair = 0
fpin = open(pairalnFile, "r")
unprocessedBuffer = ""
isEOFreached = False
processedTopoIDSet = set([])
remainedRd = None
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
if remainedRd != None:
recordList.append(remainedRd)
unprocessedBuffer = myfunc.ReadFastaFromBuffer(
buff, recordList, isEOFreached)
numRecord = len(recordList)
if numRecord > 0:
cntSelectedPair += SelectRecord(recordList, pairlistSet, fpout)
if cntSelectedPair >= numPairToSelect:
break
if numRecord % 2 == 1:
remainedRd = recordList[numRecord - 1]
else:
remainedRd = None
if isEOFreached == True:
break
fpin.close()
except IOError:
print >> sys.stderr, "Failed to open file %s for read" % (pairalnFile)
return 1
def FilterPairalnByKeyword(infile, seqid2AnnoDict, fpout): #{{{
try:
fpin = open(infile, "r")
unprocessedBuffer = ""
isEOFreached = False
processedTopoIDSet = set([])
remainedRd = None
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
if remainedRd != None:
recordList.append(remainedRd)
unprocessedBuffer = myfunc.ReadFastaFromBuffer(
buff, recordList, isEOFreached)
numRecord = len(recordList)
if numRecord > 0:
FilterRecord(recordList, seqid2AnnoDict, fpout)
if numRecord % 2 == 1:
remainedRd = recordList[numRecord - 1]
else:
remainedRd = None
if isEOFreached == True:
break
fpin.close()
except IOError:
print >> sys.stderr, "Failed to open file %s for read" % (infile)
return 1
def MSA2Seq_fasta(infile, outfile): #{{{
try:
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
fpin = open(infile, "rb")
unprocessedBuffer = ""
isEOFreached = False
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(
buff, recordList, isEOFreached)
for rd in recordList:
anno = rd[1]
seq = rd[2].replace("-", "").replace(".", "").replace(" ", "")
fpout.write(">%s\n" % anno)
fpout.write("%s\n" % seq)
if isEOFreached == True:
break
fpin.close()
myfunc.myclose(fpout)
except IOError:
print >> sys.stderr, "Failed to read file", infile
return 1
rundir = os.path.dirname(__file__)
basedir = os.path.realpath("%s/../" % (rundir))
if 0: #{{{
infile = sys.argv[1]
li = myfunc.ReadIDList2(infile, 2, None)
print(li)
#}}}
if 0: #{{{
rawseq = ">1\nseqAAAAAAAAAAAAAAAAAAAAAAAAA\n \n>2 dad\ndfasdf "
#rawseq = " >1\nskdfaskldgasdk\nf\ndadfa\n\n\nadsad \n"
#rawseq = ">sadjfasdkjfsalkdfsadfjasdfk"
rawseq = "asdkfjasdg asdkfasdf\n"
seqRecordList = []
myfunc.ReadFastaFromBuffer(rawseq, seqRecordList, True, 0, 0)
print(seqRecordList)
#}}}
if 0: #{{{
size = float(sys.argv[1])
print("size=", size)
print("humansize=", myfunc.Size_byte2human(size)) #}}}
if 0: # {{{
newsfile = "%s/static/doc/news.txt" % (basedir)
newsList = myfunc.ReadNews(newsfile)
print(newsList)
# }}}
def main(g_params):#{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
mapfile = ""
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
infile = sys.argv[i+1]
isNonOptionArg=False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg=True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] == "-h" or sys.argv[i] == "--help":
PrintHelp()
return 1
elif sys.argv[i] in [ "-i", "--i", "--infile"]:
infile = sys.argv[i+1]
i = i + 2
elif sys.argv[i] in [ "-o", "--o", "-outfile", "--outfile"]:
outfile =sys.argv[i+1]
i = i + 2
elif sys.argv[i] in [ "-map", "--map"]:
mapfile =sys.argv[i+1]
i = i + 2
else:
print >> sys.stderr,("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
infile = sys.argv[i]
i+=1
if infile == "":
print >> sys.stderr,"Error! Topology file not set."
return 1
isMapSupplied = False
mapDict = {}
if mapfile != "" and os.path.exists(mapfile):
mapDict = ReadMapFile(mapfile)
isMapSupplied = True
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
try:
fpin = open (infile, "rb")
unprocessedBuffer=""
isEOFreached = False
processedTopoIDSet = set([])
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached=True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff,recordList, isEOFreached)
if len(recordList) > 0:
for rd in recordList:
# if not isMapSupplied use seqid as the first word
# else, using mapped id, and if keyerror, use the original annotation line
if not isMapSupplied:
renamedID = rd[0]
fpout.write(">%s %s\n"%(renamedID, rd[1]))
else:
try:
renamedID = mapDict[rd[0]]
fpout.write(">%s %s\n"%(renamedID, rd[1]))
except KeyError:
msg = "ID %s not found in mapDict"
print >> sys.stderr, msg%(rd[0])
fpout.write(">%s\n"%(rd[1]))
fpout.write("%s\n"%(rd[2]))
if isEOFreached == True:
break
fpin.close()
except IOError:
print >> sys.stderr, "Failed to read input file %s"%(infile)
return 1
myfunc.myclose(fpout)
def main():#{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
global isPrintSeqID
outFile=""
inFile=""
fastaFile=""
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg=False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg=True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] == "-h" or sys.argv[i] == "--help":
PrintHelp()
return 1
elif sys.argv[i] == "-i" or sys.argv[i] == "--infile":
inFile=sys.argv[i+1]
i = i + 2
elif sys.argv[i] == "-f" or sys.argv[i] == "--fasta":
fastaFile=sys.argv[i+1]
i = i + 2
elif sys.argv[i] == "-printid" or sys.argv[i] == "--printid":
if (sys.argv[i+1].lower())[0] == "y":
isPrintSeqID=True
else:
isPrintSeqID=False
i = i + 2
elif sys.argv[i] == "-o" or sys.argv[i] == "--outfile":
outFile=sys.argv[i+1]
i = i + 2
else:
print >> sys.stderr,("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
inFile=sys.argv[i]
i+=1
if inFile == "":
print >> sys.stderr,"Error! Topology file not set."
return 1
if fastaFile == "":
print >> sys.stderr,"Error! amino acid fasta file not set."
return 1
fpout = sys.stdout
if outFile != "":
fpout = open(outFile,"w")
if not fpout:
print >> sys.stderr, "Failed to write to outfile %s. "%(outFile)
print >> sys.stderr, "Reset output to stdout."
fpout = sys.stdout
sizeAASeqFile = os.path.getsize(fastaFile)
if sizeAASeqFile > MAX_FASTA_AA_FILE_SIZE:
print >> sys.stderr, ("size (%d)"%sizeAASeqFile
+ " of fasta sequence file (%s)"%fastaFile
+ " is over the limit (%d). Exit."% MAX_FASTA_AA_FILE_SIZE)
return 1
(idListSeq, annotationListSeq, seqList) = myfunc.ReadFasta(fastaFile)
if idListSeq == None:
print >> sys.stderr, "%s exit with error."%sys.argv[0]
return 1
elif idListSeq < 1:
print >> sys.stderr, ("Warning! zero aa sequences have"
+ " been read in for file %s" %fastaFile)
aaSeqDict={}
for i in xrange (len(idListSeq)):
aaSeqDict[idListSeq[i]] = seqList[i]
fpin = open (inFile, "rb")
if not fpin:
print >> sys.stderr, "Failed to open input file %s"%(inFile)
return -1
unprocessedBuffer=""
isEOFreached = False
processedTopoIDSet = set([])
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached=True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff,recordList, isEOFreached)
if len(recordList) > 0:
idListTopo = [r[0] for r in recordList]
topoList = [r[2] for r in recordList]
Topo2TMFrag(idListTopo, topoList,aaSeqDict, processedTopoIDSet, fpout)
if isEOFreached == True:
break
fpin.close()
if fpout != None and fpout != sys.stdout:
fpout.close()
def main(): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
inFile = ""
dgFile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] == "-h" or sys.argv[i] == "--help":
PrintHelp()
return 1
elif sys.argv[i] == "-i" or sys.argv[i] == "--infile":
inFile = sys.argv[i + 1]
i = i + 2
elif sys.argv[i] == "-dg" or sys.argv[i] == "--dg":
dgFile = sys.argv[i + 1]
i = i + 2
elif sys.argv[i] == "-outpath" or sys.argv[i] == "--outpath":
outpath = sys.argv[i + 1]
i = i + 2
else:
print >> sys.stderr, ("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
inFile = sys.argv[i]
i += 1
if inFile == "":
print >> sys.stderr, "Error! Topology file not set."
return 1
if dgFile == "":
print >> sys.stderr, "Error! dgFile not set."
return 1
os.system("mkdir -p %s" % outpath)
dgScoreDict = lcmp.ReadDGScore(dgFile)
if dgScoreDict == {}:
print >> sys.stderr, "Read DG score failed. exit"
return 1
rootname = os.path.basename(os.path.splitext(inFile)[0])
outFileTopoDG = outpath + os.sep + rootname + ".topowithdgscore"
fpTopoDG = myfunc.myopen(outFileTopoDG, None, "w", False)
if fpTopoDG == None:
return 1
fpin = open(inFile, "rb")
if not fpin:
print >> sys.stderr, "Failed to open input file %s" % (inFile)
return -1
unprocessedBuffer = ""
isEOFreached = False
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff, recordList,
isEOFreached)
if len(recordList) > 0:
idListTopo = [r[0] for r in recordList]
annotationListTopo = [r[1] for r in recordList]
topoList = [r[2] for r in recordList]
TopoAddDGscore(idListTopo, annotationListTopo, topoList,
dgScoreDict, fpTopoDG)
if isEOFreached == True:
break
myfunc.myclose(fpTopoDG)
print outFileTopoDG, "output"
def main(g_params): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outFile = ""
idList = []
idListFile = ""
fastaFile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
idList.append(sys.argv[i])
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if (sys.argv[i] in ["-h", "--help"]):
PrintHelp()
return 1
elif (sys.argv[i] in ["-l", "--l", "-list", "--list"]):
idListFile = sys.argv[i + 1]
i = i + 2
elif (sys.argv[i] in ["-f", "--f", "-fasta", "--fasta"]):
fastaFile = sys.argv[i + 1]
i = i + 2
elif (sys.argv[i] in ["-o", "--o", "-outfile", "--outfile"]):
outFile = sys.argv[i + 1]
i = i + 2
elif (sys.argv[i] in ["-mine", "--mine"]):
g_params['min_evalue'] = float(sys.argv[i + 1])
g_params['isEvalueSet'] = True
i = i + 2
elif (sys.argv[i] in ["-maxe", "--maxe"]):
g_params['max_evalue'] = float(sys.argv[i + 1])
g_params['isEvalueSet'] = True
i = i + 2
else:
print(("Error! Wrong argument:%s" % sys.argv[i]),
file=sys.stderr)
return 1
else:
idList.append(sys.argv[i])
i += 1
if fastaFile == "":
print("Fatal! fasta file not set. Exit.", file=sys.stderr)
return 1
elif not os.path.exists(fastaFile):
print("Fatal! fasta file %s does not exist. Exit." % (fastaFile),
file=sys.stderr)
return 1
if os.path.exists(idListFile):
idList += myfunc.ReadIDList(idListFile)
if len(idList) > 0:
isIDSet = True
else:
isIDSet = False
if not g_params['isEvalueSet'] and not isIDSet:
print("Error! no ID nor evalue threshold is set. Eixt",
file=sys.stderr)
return 1
idListSet = set(idList)
fpout = myfunc.myopen(filename=outFile,
default_fp=sys.stdout,
mode="w",
isRaise=False)
fpin = open(fastaFile, "r")
if not fpin:
print("Failed to open fastafile %s" % (fastaFile), file=sys.stderr)
return -1
unprocessedBuffer = ""
isEOFreached = False
BLOCK_SIZE = g_params['BLOCK_SIZE']
isEvalueSet = g_params['isEvalueSet']
min_evalue = g_params['min_evalue']
max_evalue = g_params['max_evalue']
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff, recordList,
isEOFreached)
if len(recordList) > 0:
for r in recordList:
if ((not isIDSet) or (r[0] in idListSet)):
if (not isEvalueSet or r[1].lower().find('evalue') < 0):
fpout.write(">%s\n" % r[1])
fpout.write("%s\n" % r[2])
else:
evalue = myfunc.GetEvalueFromAnnotation(r[1])
if (evalue == None or
(evalue >= min_evalue and evalue <= max_evalue)):
fpout.write(">%s\n" % r[1])
fpout.write("%s\n" % r[2])
if isEOFreached == True:
break
fpin.close()
myfunc.myclose(fpout)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
seqdbfile = ""
infile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = argv[i]
isNonOptionArg = False
i += 1
elif argv[i] == "--":
isNonOptionArg = True
i += 1
elif argv[i][0] == "-":
if argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in ["-outfile", "--outfile"]:
outfile = argv[i + 1]
i += 2
elif argv[i] in ["-seqdb", "--seqdb"]:
seqdbfile = argv[i + 1]
i += 2
elif argv[i] in ["-q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
infile = argv[i]
i += 1
if infile == "":
print >> sys.stderr, "topofile not set"
return 1
elif not os.path.exists(infile):
print >> sys.stderr, "topofile %s does not exist" % (infile)
return 1
# if seqdbfile == "":
# print >> sys.stderr, "seqdbfile file not set"
# return 1
# elif not os.path.exists(seqdbfile):
# print >> sys.stderr, "seqdbfile file %s does not exist"%(seqdbfile)
# return 1
# seqDict = GetSeqDict(seqdbfile)
# if seqDict == {}:
# print >> sys.stderr, "Failed to read seqdbfile %s"%(seqdbfile)
# return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
fpin = open(infile, "rb")
if not fpin:
print >> sys.stderr, "Failed to open input file %s" % (infile)
return 1
unprocessedBuffer = ""
unprocessedRecordList = []
isEOFreached = False
processedTopoIDSet = set([])
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = unprocessedRecordList
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff, recordList,
isEOFreached)
numRecord = len(recordList)
if numRecord > 0:
numPair = numRecord / 2
for i in xrange(numPair):
rd1 = recordList[2 * i]
rd2 = recordList[2 * i + 1]
id1 = rd1[0]
topo1 = rd1[2]
id2 = rd2[0]
topo2 = rd2[2]
stat1 = GetTopoAlignStat(topo1, topo2)
stat2 = GetTopoAlignStat(topo2, topo1)
WriteStat(id1, id2, stat1, fpout)
WriteStat(id2, id1, stat1, fpout)
if numRecord % 2 == 1:
unprocessedRecordList = [recordList[-1]]
else:
unprocessedRecordList = []
if isEOFreached == True:
break
fpin.close()
myfunc.myclose(fpout)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
seqdbfile = ""
infile = ""
i = 1
isNonOptionArg=False
while i < numArgv:
if isNonOptionArg == True:
infile = argv[i]
isNonOptionArg = False
i += 1
elif argv[i] == "--":
isNonOptionArg = True
i += 1
elif argv[i][0] == "-":
if argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif argv[i] in ["-outfile", "--outfile"]:
outfile = argv[i+1]
i += 2
elif argv[i] in ["-seqdb", "--seqdb"]:
seqdbfile = argv[i+1]
i += 2
elif argv[i] in ["-q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
infile = argv[i]
i += 1
if infile == "":
print >> sys.stderr, "topofile not set"
return 1
elif not os.path.exists(infile):
print >> sys.stderr, "topofile %s does not exist"%(infile)
return 1
# if seqdbfile == "":
# print >> sys.stderr, "seqdbfile file not set"
# return 1
# elif not os.path.exists(seqdbfile):
# print >> sys.stderr, "seqdbfile file %s does not exist"%(seqdbfile)
# return 1
# seqDict = GetSeqDict(seqdbfile)
# if seqDict == {}:
# print >> sys.stderr, "Failed to read seqdbfile %s"%(seqdbfile)
# return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
fpin = open (infile, "rb");
if not fpin:
print >> sys.stderr, "Failed to open input file %s"%(infile)
return 1
unprocessedBuffer="";
isEOFreached = False;
processedTopoIDSet = set([]);
while 1:
buff = fpin.read(BLOCK_SIZE);
if len(buff) < BLOCK_SIZE:
isEOFreached=True;
buff = unprocessedBuffer + buff;
recordList = [];
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff,recordList, isEOFreached);
if len(recordList) > 0:
idListTopo = [r[0] for r in recordList];
topoList = [r[2] for r in recordList];
for i in xrange(len(idListTopo)):
seqid = idListTopo[i]
topo = topoList[i]
posTM = myfunc.GetTMPosition(topo)
if len(posTM) > 0:
cnt = 0
for (b,e) in posTM:
seg = topo[b:e]
fpout.write("%s\t%4d\t%s\n"%(seqid, cnt+1, seg))
cnt += 1
if isEOFreached == True:
break;
fpin.close();
myfunc.myclose(fpout)
def main(g_params): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
isQuiet = False
isPrintIDName = True
outfile = ""
topofile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
topofile = sys.argv[i]
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] in ["-h", "--help"]:
PrintHelp()
return 1
elif sys.argv[i] in ["-o", "--o", "-out"]:
outfile = sys.argv[i + 1]
i = i + 2
elif sys.argv[i] in ["-q", "--q"]:
isQuiet = True
i = i + 1
elif sys.argv[i] in ["-ni", "--ni", "-noid"]:
isPrintIDName = False
i = i + 1
else:
print "Error! Wrong argument:", sys.argv[i]
return 1
else:
topofile = sys.argv[i]
i = i + 1
if topofile == "":
print >> sys.stderr, "topofile not set. Exit."
return 1
elif not os.path.exists(topofile):
print >> sys.stderr, "topofile %s doe not exist. Exit." % topofile
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
fpin = open(topofile, "rb")
if not fpin:
print >> sys.stderr, "Failed to open input file %s" % (topofile)
return 1
unprocessedBuffer = ""
isEOFreached = False
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff, recordList,
isEOFreached)
if len(recordList) > 0:
for rd in recordList:
if isPrintIDName:
fpout.write("%s\t" % rd[0])
fpout.write("%d\n" % myfunc.CountTM(rd[2]))
if isEOFreached == True:
break
fpin.close()
myfunc.myclose(fpout)
return 0
def ValidateSeq(rawseq, seqinfo, g_params): #{{{
# seq is the chunk of fasta file
# seqinfo is a dictionary
# return (filtered_seq)
rawseq = re.sub(r'[^\x00-\x7f]', r' ',
rawseq) # remove non-ASCII characters
rawseq = re.sub(r'[\x0b]', r' ',
rawseq) # filter invalid characters for XML
filtered_seq = ""
# initialization
for item in ['errinfo_br', 'errinfo', 'errinfo_content', 'warninfo']:
if item not in seqinfo:
seqinfo[item] = ""
seqinfo['isValidSeq'] = True
seqRecordList = []
myfunc.ReadFastaFromBuffer(rawseq, seqRecordList, True, 0, 0)
# filter empty sequences and any sequeces shorter than MIN_LEN_SEQ or longer
# than MAX_LEN_SEQ
newSeqRecordList = []
li_warn_info = []
isHasEmptySeq = False
isHasShortSeq = False
isHasLongSeq = False
isHasDNASeq = False
cnt = 0
for rd in seqRecordList:
seq = rd[2].strip()
seqid = rd[0].strip()
if len(seq) == 0:
isHasEmptySeq = 1
msg = "Empty sequence %s (SeqNo. %d) is removed." % (seqid,
cnt + 1)
li_warn_info.append(msg)
elif len(seq) < g_params['MIN_LEN_SEQ']:
isHasShortSeq = 1
msg = "Sequence %s (SeqNo. %d) is removed since its length is < %d." % (
seqid, cnt + 1, g_params['MIN_LEN_SEQ'])
li_warn_info.append(msg)
elif len(seq) > g_params['MAX_LEN_SEQ']:
isHasLongSeq = True
msg = "Sequence %s (SeqNo. %d) is removed since its length is > %d." % (
seqid, cnt + 1, g_params['MAX_LEN_SEQ'])
li_warn_info.append(msg)
elif myfunc.IsDNASeq(seq):
isHasDNASeq = True
msg = "Sequence %s (SeqNo. %d) is removed since it looks like a DNA sequence." % (
seqid, cnt + 1)
li_warn_info.append(msg)
else:
newSeqRecordList.append(rd)
cnt += 1
seqRecordList = newSeqRecordList
numseq = len(seqRecordList)
if numseq < 1:
seqinfo['errinfo_br'] += "Number of input sequences is 0!\n"
t_rawseq = rawseq.lstrip()
if t_rawseq and t_rawseq[0] != '>':
seqinfo[
'errinfo_content'] += "Bad input format. The FASTA format should have an annotation line start with '>'.\n"
if len(li_warn_info) > 0:
seqinfo['errinfo_content'] += "\n".join(li_warn_info) + "\n"
if not isHasShortSeq and not isHasEmptySeq and not isHasLongSeq and not isHasDNASeq:
seqinfo[
'errinfo_content'] += "Please input your sequence in FASTA format.\n"
seqinfo['isValidSeq'] = False
elif numseq > g_params['MAX_NUMSEQ_PER_JOB']:
seqinfo[
'errinfo_br'] += "Number of input sequences exceeds the maximum (%d)!\n" % (
g_params['MAX_NUMSEQ_PER_JOB'])
seqinfo[
'errinfo_content'] += "Your target sequence field has %d sequences. " % (
numseq)
seqinfo[
'errinfo_content'] += "However, the maximal allowed sequences for this field is %d. " % (
g_params['MAX_NUMSEQ_PER_JOB'])
#seqinfo['errinfo_content'] += "Please split your query into smaller files and submit again.\n"
seqinfo['isValidSeq'] = False
else:
li_badseq_info = []
if 'isForceRun' in seqinfo and seqinfo[
'isForceRun'] and numseq > g_params['MAX_NUMSEQ_FOR_FORCE_RUN']:
seqinfo['errinfo_br'] += "Invalid input!"
seqinfo['errinfo_content'] += "You have chosen the \"Force Run\" mode. "\
"The maximum allowable number of sequences of a job is %d. "\
"However, your input has %d sequences."%(g_params['MAX_NUMSEQ_FOR_FORCE_RUN'], numseq)
seqinfo['isValidSeq'] = False
# checking for bad sequences in the query
if seqinfo['isValidSeq']:
for i in xrange(numseq):
seq = seqRecordList[i][2].strip()
anno = seqRecordList[i][1].strip().replace('\t', ' ')
seqid = seqRecordList[i][0].strip()
seq = seq.upper()
seq = re.sub("[\s\n\r\t]", '', seq)
li1 = [
m.start()
for m in re.finditer("[^ABCDEFGHIKLMNPQRSTUVWYZX*-]", seq)
]
if len(li1) > 0:
for j in xrange(len(li1)):
msg = "Bad letter for amino acid in sequence %s (SeqNo. %d) "\
"at position %d (letter: '%s')"%(seqid, i+1,
li1[j]+1, seq[li1[j]])
li_badseq_info.append(msg)
if len(li_badseq_info) > 0:
seqinfo[
'errinfo_br'] += "There are bad letters for amino acids in your query!\n"
seqinfo['errinfo_content'] = "\n".join(li_badseq_info) + "\n"
seqinfo['isValidSeq'] = False
# convert some non-classical letters to the standard amino acid symbols
# Scheme:
# out of these 26 letters in the alphabet,
# B, Z -> X
# U -> C
# *, - will be deleted
if seqinfo['isValidSeq']:
li_newseq = []
for i in xrange(numseq):
seq = seqRecordList[i][2].strip()
anno = seqRecordList[i][1].strip()
seqid = seqRecordList[i][0].strip()
seq = seq.upper()
seq = re.sub("[\s\n\r\t]", '', seq)
anno = anno.replace('\t', ' ') #replace tab by whitespace
li1 = [m.start() for m in re.finditer("[BZ]", seq)]
if len(li1) > 0:
for j in xrange(len(li1)):
msg = "Amino acid in sequence %s (SeqNo. %d) at position %d "\
"(letter: '%s') has been replaced by 'X'"%(seqid,
i+1, li1[j]+1, seq[li1[j]])
li_warn_info.append(msg)
seq = re.sub("[BZ]", "X", seq)
li1 = [m.start() for m in re.finditer("[U]", seq)]
if len(li1) > 0:
for j in xrange(len(li1)):
msg = "Amino acid in sequence %s (SeqNo. %d) at position %d "\
"(letter: '%s') has been replaced by 'C'"%(seqid,
i+1, li1[j]+1, seq[li1[j]])
li_warn_info.append(msg)
seq = re.sub("[U]", "C", seq)
li1 = [m.start() for m in re.finditer("[*]", seq)]
if len(li1) > 0:
for j in xrange(len(li1)):
msg = "Translational stop in sequence %s (SeqNo. %d) at position %d "\
"(letter: '%s') has been deleted"%(seqid,
i+1, li1[j]+1, seq[li1[j]])
li_warn_info.append(msg)
seq = re.sub("[*]", "", seq)
li1 = [m.start() for m in re.finditer("[-]", seq)]
if len(li1) > 0:
for j in xrange(len(li1)):
msg = "Gap in sequence %s (SeqNo. %d) at position %d "\
"(letter: '%s') has been deleted"%(seqid,
i+1, li1[j]+1, seq[li1[j]])
li_warn_info.append(msg)
seq = re.sub("[-]", "", seq)
# check the sequence length again after potential removal of
# translation stop
if len(seq) < g_params['MIN_LEN_SEQ']:
isHasShortSeq = 1
msg = "Sequence %s (SeqNo. %d) is removed since its length is < %d (after removal of translation stop)." % (
seqid, i + 1, g_params['MIN_LEN_SEQ'])
li_warn_info.append(msg)
else:
li_newseq.append(">%s\n%s" % (anno, seq))
filtered_seq = "\n".join(li_newseq) # seq content after validation
seqinfo['numseq'] = len(li_newseq)
seqinfo['warninfo'] = "\n".join(li_warn_info) + "\n"
seqinfo['errinfo'] = seqinfo['errinfo_br'] + seqinfo['errinfo_content']
return filtered_seq
def main(): #{{{
if 0: #{{{
strTop1 = "---MMMM-----i-i-i---MMM----MMMM-ooo"
strTop2 = "----MMMM-----i-ii-----MMM---MMM--oo"
strProtein1 = "id1"
strProtein2 = "id2"
fpLog = sys.stdout
class_gapless, num1_gapless, num2_gapless = ct.CompareToposGaplesslyNew(
strTop1, strTop2, strProtein1, strProtein2, fpLog)
# Note: calling the int, float, string will not change their original value
# calling the dict, list will change their original value
print "strTop1:", strTop1
print "strTop2:", strTop2
#}}}
if 0: #{{{
PrintFuncName()
print("this file name is: %s" % __file__)
#}}}
if 0: #{{{
# filename="/nanjiang/data/blastdb/uniprot_KW181_idt50.fasta"
filename = sys.argv[1]
print filename
fp = open(filename, "r")
lines = fp.readlines()
fp.close()
#}}}
if 0: #{{{
# filename="/nanjiang/data/blastdb/uniprot_KW181_idt50.fasta"
filename = sys.argv[1]
print filename
BLOCK_SIZE = 100000
fp = open(filename, "r")
buff = fp.read(BLOCK_SIZE)
while buff:
buff = fp.read(BLOCK_SIZE)
fp.close()
#}}}
if 0: #{{{
# filename="/nanjiang/data/blastdb/uniprot_KW181_idt50.fasta"
filename = sys.argv[1]
print filename
fp = open(filename, "r")
line = fp.readline()
while line:
line = fp.readline()
fp.close()
#}}}
if 0: #{{{
try:
BLOCK_SIZE = 100000
infile = sys.argv[1]
fpin = open(infile, 'rb')
unprocessedBuffer = ""
isEOFreached = False
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(
buff, recordList, isEOFreached)
if len(recordList) > 0:
for record in recordList:
sys.stdout.write(">%s\n" % record[1])
sys.stdout.write("%s\n" % record[2])
if isEOFreached == True:
break
fpin.close()
except IOError:
raise
#}}}
if 0: #{{{
try:
infile = sys.argv[1]
(annoList, seqList) = myfunc.ReadFasta_without_id(infile)
for i in xrange(len(seqList)):
sys.stdout.write(">%s\n" % annoList[i])
sys.stdout.write("%s\n" % seqList[i])
except IOError:
raise
#}}}
if 0: #{{{
hhrfile = "hhsearch/A1RZ92-Q74DY9.hhr"
if IsDuplicatedByHHSearch(hhrfile):
print "yes"
#}}}
if 0: #{{{
import pairlistwithfamid2pairaln_by_msa
seq1 = "--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MLSSTATTMLRAGVSRSSGALQPMLLRSAACPCSPFSMNTKLSQPTSV-----RPLSTSPSALVLRFRAQQQAQLAQQQLRRASSSSSSSSSSTRPRSDAELDANAAEAAAAAQSAAHAGEPVLDWNTFFKLRKTRRRVQLAFSVIMTLITSGAGGAVLSTGVADAMVAQVPLEPMFAVGLMTASFGALGWLMGPAMGGMVFNALKSKYRGQMEIKEGQFFARIKKHRVDPSASSMGNPVPDFYGEKISSVAGYRQWLKDQRAFNKKRTTFV"
seq2 = "MDILLAVLEQGFIFSIVCFGVYITYKILDFPDLSVDGTFPLGAAVAAAFLVKGYSPVLSSLAALVAGAIAGGITGILHVKFKITNLLSGILVMVGLYSINLRIMGKSNIPLFNKIHLFSDTMNPIIIITVFLLICKITLDLFLKTKAGFILKATGDNEQLVLSLGVNKDLVKIMGLMLSNALVALGGALMAQYQGFSDVGMGTGIVVMGLASVIIGESLFGRIKALNATTRVLLGALVYKLSVSI---ALTVGLAP-------TDLKLVTAIIVVIALSLNKNPLKIITKQKTKEGGIL------NASNTKSAQSVQ-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
seq1 = "---------------------------------------------------------------------------------------------------------------------------------------MALSSLFFTASALLLMFLAFLGGARNSNPLDRIYWLEAATGNIPGAPALSRWTYWNLCAVNSEGHNECGKSYPDYPFDPPSHRNFNTHVNIPAAFIGTRHYFLTSRFMFPFHIIALFFATCSLLTGFLAMCTRIGNWVSAFSAYFALTFQTITTCLMTAVYVQGRDKFNNNGQSSHLGVKAFAFMWTSVALLFLSCVIYCMGGAVGRKDGGYSGREQRRRGFFNSHRSGSLRSNKETAP"
seq2 = "MRKIAAIGGIVFISFILTIVAMFTKLWISWSIGKFSYGIGIVPYHSNSAGWFTAASWMVFISFGLFIPLILVVLFTAYKVHHDGCCHSIRHCFNSICLICSIIAVLEIIAFVLMAVNASRYVKGASISEKKSLLQLGSSAYLDLVSAILIIVATVLSGHASHHDCH----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
alignFactor = pairlistwithfamid2pairaln_by_msa.GetAlignmentFactorFromPairAlignment(
seq1, seq2)
print alignFactor
#}}}
if 0: #{{{
try:
dbname = sys.argv[1]
print dbname
from myfunc import MyDB
cls = MyDB(dbname)
# print cls.idList
record = cls.GetRecord("A0FGX9")
if record:
print record
# for rd in cls.GetAllRecord():
# print rd
(seqid, anno, seq) = myfunc.ExtractFromSeqWithAnno(record)
print(seqid, anno, seq)
except IndexError:
pass
#}}}
if 0: #{{{
import my_extractdb
#miniking my_extractdb.py see which one is faster
try:
dbname = sys.argv[1]
idlistfile = sys.argv[2]
cls = myfunc.MyDB(dbname)
if cls.failure:
print >> sys.stderr, "MyDB init failed"
else:
idlist = open(idlistfile, "r").read().split("\n")
fpout = sys.stdout
for seqid in idlist:
if seqid:
record = cls.GetRecord(seqid)
fpout.write(record)
# for rd in cls.GetAllRecord():
# print rd
# (seqid, anno, seq) = myfunc.ExtractFromSeqWithAnno(record)
# print (seqid, anno, seq)
except IndexError:
print "error"
pass
#}}}
if 0: #{{{ #test ReadLineByBlock
try:
infile = sys.argv[1]
from myfunc import ReadLineByBlock
cls = ReadLineByBlock(infile)
lines = cls.readlines()
while lines != None:
for line in lines:
print line
lines = cls.readlines()
except IndexError:
pass
#}}}
if 0: #{{{ #test speed of ReadLineByBlock
# ReadLineByBlock is about 3 times fater than file.readline()
try:
from myfunc import ReadLineByBlock
infile = sys.argv[1]
start = time.time()
hdl = ReadLineByBlock(infile)
lines = hdl.readlines()
while lines != None:
lines = hdl.readlines()
hdl.close()
end = time.time()
msg = "Reading %s by ReadLineByBlock costs %.3fs seconds"
print msg % (infile, (end - start))
start = time.time()
hdl = open(infile, "r")
line = hdl.readline()
while line:
line = hdl.readline()
hdl.close()
end = time.time()
msg = "Reading %s by readline() costs %.3fs seconds"
print msg % (infile, (end - start))
except IndexError:
pass
#}}}
if 0: #{{{ #test readline
try:
infile = sys.argv[1]
fp = open(infile, "r")
line = fp.readline()
while line:
print line
line = fp.readline()
fp.close()
except IndexError:
pass
#}}}
if 0: #{{{ #test the speed of GetFirstWord
try:
nloop = int(sys.argv[1])
string = "kjdafk jasdfj j"
#string = "askdf askdf "
# string = "kajsdfasdfsdfjakasjdfka"
# string = "kajsdfasdf,sdfjakasjdfka"
delimiter = " \t\r,.\n"
delimiter = " "
for i in xrange(nloop):
#firstword = myfunc.GetFirstWord(string, delimiter)
#firstword = string.split()[0]
#firstword = string.partition(" ")[0]
firstword = myfunc.GetFirstWord(string)
#pass
#print firstword
except (IndexError, ValueError):
pass
#}}}
if 0: #{{{ # read seq by SeqIO
from Bio import SeqIO
try:
seqfile = sys.argv[1]
# 1. SeqIO ####################
start = time.time()
handle = open(seqfile, "rU")
cnt = 0
for record in SeqIO.parse(handle, "fasta"):
cnt += 1
handle.close()
end = time.time()
msg = "Reading %d sequences by SeqIO costs %.3fs seconds"
print msg % (cnt, (end - start))
# 2. ReadFasta ####################
start = time.time()
seqfile = sys.argv[1]
(idList, annoList, seqList) = myfunc.ReadFasta(seqfile)
end = time.time()
msg = "Reading %d sequences by ReadFasta costs %.3fs seconds"
print msg % (len(idList), (end - start))
# 3. ReadFasta from buffer
BLOCK_SIZE = 100000
start = time.time()
cnt = 0
fpin = open(seqfile, 'rb')
unprocessedBuffer = ""
isEOFreached = False
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(
buff, recordList, isEOFreached)
cnt += len(recordList)
if isEOFreached == True:
break
fpin.close()
end = time.time()
msg = "Reading %d sequences by ReadFastaFromBuffer costs %.3fs seconds"
print msg % (cnt, (end - start))
# 4. ReadFastaByBlock ####################
start = time.time()
seqfile = sys.argv[1]
hdl = myfunc.ReadFastaByBlock(seqfile, 0, 0)
if hdl.failure:
print >> sys.stderr, "Failed to init ReadFastaByBlock"
return 1
recordList = hdl.readseq()
cnt = 0
while recordList != None:
cnt += len(recordList)
# for rd in recordList:
# print ">%s"%rd.description
# print rd.seq
recordList = hdl.readseq()
hdl.close()
end = time.time()
msg = "Reading %d sequences by ReadFastaByBlock costs %.3fs seconds"
print msg % (cnt, (end - start))
except (IndexError, ValueError):
pass
#}}}
if 0: #{{{ #test RemoveUnnecessaryGap
try:
infile = sys.argv[1]
start = time.time()
(idList, seqList) = myfunc.ReadFasta_without_annotation(infile)
seqList = lcmp.RemoveUnnecessaryGap_old(seqList)
end = time.time()
msg = "Run RemoveUnnecessaryGap_old for %s costs %.3fs seconds"
print >> sys.stderr, msg % (infile, (end - start))
for seq in seqList:
print seq
start = time.time()
(idList, seqList) = myfunc.ReadFasta_without_annotation(infile)
seqList = lcmp.RemoveUnnecessaryGap(seqList)
end = time.time()
msg = "Run RemoveUnnecessaryGap for %s costs %.3fs seconds"
print >> sys.stderr, msg % (infile, (end - start))
for seq in seqList:
print seq
except IndexError:
pass
#}}}
if 0: #{{{ #test ReadMPAByBlock
try:
infile = sys.argv[1]
hdl = myfunc.ReadMPAByBlock(infile)
if hdl.failure:
return
recordList = hdl.readseq()
while recordList != None:
for rd in recordList:
#print rd.seqid
print ">%s" % (rd.description)
print "%s" % (myfunc.mpa2seq(rd.mpa))
recordList = hdl.readseq()
hdl.close()
except IndexError:
pass
#}}}
if 0: #{{{
try:
dbname = sys.argv[1]
print dbname
from myfunc import MyDB
cls = MyDB(dbname)
# print cls.idList
record = cls.GetRecord("A0FGX9")
if record:
print record
# for rd in cls.GetAllRecord():
# print rd
(seqid, anno, seq) = myfunc.ExtractFromSeqWithAnno(record)
print(seqid, anno, seq)
except IndexError:
pass
#}}}
if 0: #{{{ #test subprocess
import glob
#invoke shell explicitly, not very good, may have security problems
subprocess.call("seq 10", shell=True)
subprocess.call("echo wait for 2 seconds...; sleep 2", shell=True)
subprocess.call("ls topo*.py", shell=True)
if 1: #{{{ #test subprocess
import glob
#invoke shell implicitly, recommended way
subprocess.call(["seq", "10"], shell=False)
subprocess.call(["echo", "wait for 1 seconds..."])
subprocess.call(["sleep", "1"])
try:
print subprocess.check_call(["ls",
"topo*.py"]) #This will not work
except subprocess.CalledProcessError, e:
print "error message:", e
subprocess.call(["ls"] + glob.glob("topo*.py"))
def main(): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = sys.argv[i]
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] == "-h" or sys.argv[i] == "--help":
PrintHelp()
return 1
elif sys.argv[i] in ["-o", "--o"]:
outfile = sys.argv[i + 1]
i = i + 2
else:
print >> sys.stderr, ("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
infile = sys.argv[i]
i += 1
if infile == "":
print >> sys.stderr, "Error! MSA file not set."
return 1
elif not os.path.exists(infile):
print >> sys.stderr, "Error! MSA file %s does not exist." % (infile)
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
isFirstSeqSet = False
targetSeqID = ""
targetSeqAnno = ""
targetSeq = ""
targetSeqBeg = 0
#starting position in alignment without terminal gaps
targetSeqEnd = 0
fpin = open(infile, "rb")
if not fpin:
print >> sys.stderr, "Failed to open input file %s" % (infile)
return -1
unprocessedBuffer = ""
isEOFreached = False
processedTopoIDSet = set([])
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff, recordList,
isEOFreached)
if len(recordList) > 0:
if not isFirstSeqSet:
targetSeqID = recordList[0][0]
targetSeqAnno = recordList[0][1]
targetSeq = recordList[0][2]
if not targetSeqID == "target":
print >> sys.stderr, "Error, the first sequence is not target sequence in file %s" % (
infile)
return 1
(targetSeqBeg,
targetSeqEnd) = GetPositionTermGapless(targetSeq)
isFirstSeqSet = True
for rd in recordList:
print >> fpout, ">%s" % (rd[1])
print >> fpout, "%s" % (rd[2][targetSeqBeg:targetSeqEnd])
if isEOFreached == True:
break
fpin.close()
myfunc.myclose(fpout)
def main(): #{{{
numArgv = len(sys.argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
infile = sys.argv[i]
isNonOptionArg = False
i = i + 1
elif sys.argv[i] == "--":
isNonOptionArg = True
i = i + 1
elif sys.argv[i][0] == "-":
if sys.argv[i] == "-h" or sys.argv[i] == "--help":
PrintHelp()
return 1
elif sys.argv[i] in ["-o", "--o"]:
outfile = sys.argv[i + 1]
i = i + 2
else:
print >> sys.stderr, ("Error! Wrong argument:%s" % sys.argv[i])
return 1
else:
infile = sys.argv[i]
i += 1
if infile == "":
print >> sys.stderr, "Error! MSA file not set."
return 1
elif not os.path.exists(infile):
print >> sys.stderr, "Error! MSA file %s does not exist." % (infile)
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
isFirstSeqSet = False
targetSeqID = ""
targetSeq = ""
trimmedSeqPosList = [] #segment list after removal of gaps in
#the target sequence
trimmedseqLength = 0
fpin = open(infile, "rb")
if not fpin:
print >> sys.stderr, "Failed to open input file %s" % (infile)
return -1
unprocessedBuffer = ""
isEOFreached = False
processedTopoIDSet = set([])
cntseq = 0
while 1:
buff = fpin.read(BLOCK_SIZE)
if len(buff) < BLOCK_SIZE:
isEOFreached = True
buff = unprocessedBuffer + buff
recordList = []
unprocessedBuffer = myfunc.ReadFastaFromBuffer(buff, recordList,
isEOFreached)
if len(recordList) > 0:
if not isFirstSeqSet:
targetSeqID = recordList[0][0]
targetSeq = recordList[0][2]
if not targetSeqID == "target":
print >> sys.stderr, "Error, the first sequence is not target sequence in file %s" % (
infile)
return 1
trimmedSeqPosList = GetTrimmedPosition(targetSeq)
lengthSegList = [(e - b) for (b, e) in trimmedSeqPosList]
trimmedseqLength = sum(lengthSegList)
trimmedseqLength = 100
isFirstSeqSet = True
for rd in recordList:
desp = ""
if rd[0] == "target":
desp = "target/1-%d" % (trimmedseqLength)
else:
cntseq += 1
desp = "sequence%07d/1-%d" % (cntseq, trimmedseqLength)
slist = [rd[2][p[0]:p[1]] for p in trimmedSeqPosList]
trimmedseq = "".join(slist)
trimmedseq = trimmedseq.replace("X", GAP)
print >> fpout, ">%s" % (desp)
print >> fpout, "%s" % (trimmedseq)
if isEOFreached == True:
break
fpin.close()
myfunc.myclose(fpout)