def GetTopoDict(topoDB, idList):
hdl = myfunc.MyDB(topoDB)
if hdl.failure:
return {}
dt = {}
for seqid in idList:
data = hdl.GetRecord(seqid)
if data:
(tmp_id, tmp_anno, tmp_seq) = myfunc.ExtractFromSeqWithAnno(data)
dt[seqid] = tmp_seq
hdl.close()
return dt
def createHitDB(pfamList, prot_name, work_dir):
hdl = myfunc.MyDB(cddseqdb)
if hdl.failure:
print "Error"
return 1
with open(work_dir + prot_name + ".hits.db.temp", "w") as outFile:
for pfamid in pfamList:
record = hdl.GetRecord(pfamid)
if record:
outFile.write(record)
hdl.close()
os.system("python my_uniqueseq.py " + work_dir + prot_name +
".hits.db.temp")
def createHitDB_mydb(pfamList, prot_name, work_dir, pfamseqdb): # {{{
"""Create the blast seqdb from pfam_scan hits, using the MyDB version of pfamfullseqdb"""
outfile_seqdb = os.path.join(work_dir, prot_name + ".hits.db.temp")
hdl = myfunc.MyDB(pfamseqdb)
if hdl.failure:
print("Failed to open pfamseqdb %s with MyDB()" % (pfamseqdb))
return 1
with open(outfile_seqdb, "w") as outFile:
for pfamid in pfamList:
record = hdl.GetRecord(pfamid)
if record:
outFile.write(record)
hdl.close()
os.system("python my_uniqueseq.py " + outfile_seqdb)
def MatchMSATopo_using_topodb(
msafile,
topodb,
isIgnoreBadseq, #{{{
method_match,
outfile):
hdl_topo = myfunc.MyDB(topodb)
if hdl_topo.failure:
return 1
hdl = myfunc.ReadFastaByBlock(msafile)
if hdl.failure:
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
recordList = hdl.readseq()
while recordList != None:
for rd in recordList:
topowithanno = hdl_topo.GetRecord(rd.seqid)
if topowithanno != None:
(topoid, topoanno,
topo) = myfunc.ExtractFromSeqWithAnno(topowithanno)
else:
print("topo not found for ID %s" % (rd.seqid), file=sys.stderr)
topo = ""
matchedtopo = MatchSeqToTopo(rd.seq, topo, method_match)
if not (matchedtopo == "BADSEQ" and isIgnoreBadseq):
print(">%s" % (rd.description), file=fpout)
print("%s" % (matchedtopo), file=fpout)
recordList = hdl.readseq()
myfunc.myclose(fpout)
hdl.close()
hdl_topo.close()
return 0
except subprocess.CalledProcessError, e:
print e
return 1
if myfunc.checkfile(pfamid2seqidFile, "pfamid2seqidFile") != 0:
return 1
if myfunc.checkfile("%s0.db" % topodb, "topodb") != 0:
return 1
if myfunc.checkfile("%s0.db" % seqdb, "seqdb") != 0:
return 1
pfamid2seqidDict = myfunc.ReadFam2SeqidMap(pfamid2seqidFile)
hdl_topo = myfunc.MyDB(topodb)
if not hdl_topo.failure:
idSet_topo = set(hdl_topo.indexedIDList)
else:
idSet_topo = set([])
print >> sys.stderr, "Failed to open topology database %s" % (topodb)
return 1
hdl_seq = myfunc.MyDB(seqdb)
if hdl_seq.failure:
print >> sys.stderr, "Failed to open sequence database %s" % (seqdb)
return 1
GetTMProList_per_family(pfamid2seqidDict, idSet_topo, hdl_seq, hdl_topo,
outpath)
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
SPE_PAIR_LIST = [(2, 1), (2, 4), (2, 6), (2, 8), (3, 6), (3, 7), (4, 6),
(4, 8), (4, 10), (5, 7), (5, 10), (6, 8), (6, 10),
(6, 12), (7, 14), (8, 10), (8, 12), (10, 12), (10, 13),
(11, 13), (12, 14)]
outfile = ""
infile = ""
pfamDefFile = "%s/data/pfam/pfam26.0/Pfam-A.clans.tsv" % (DATADIR3)
signalpFile = "%s/wk/MPTopo/pfamAna_refpro/pred_signalp/refpro20120604-celluar.selmaxlength-m1.nr100.signalp_list" % (
DATADIR3)
#seqid2clanidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.seqid2clanid"%(DATADIR3)
#seqid2pfamidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.seqid2pfamid"%(DATADIR3)
seqid2clanidMapFile = ""
seqid2pfamidMapFile = ""
tm_pfamidListFile = ""
tm_clanidListFile = ""
pfamid2seqidMapFile = ""
clanid2seqidMapFile = ""
dbname_predTM = ""
pairlistwithpfamidFile = ""
pfamtype = ""
pairListFile = ""
#classList_TableNumTMHeatMap = ["ALL", "RMSP"]
classList_TableNumTMHeatMap = ["ALL"]
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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outpath", "--outpath"]:
(g_params['outpath'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"]:
(fileListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pfamdef", "--pfamdef"]:
(pfamDefFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-signalp", "--signalp"]:
(signalpFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-mp", "--mp"]:
g_params[
'pairwise_comparison_method'], i = myfunc.my_getopt_int(
argv, i)
elif argv[i] in ["-mindiffpair", "--mindiffpair"]:
g_params['mindiffpair'], i = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-pfamtype", "--pfamtype"]:
pfamtype, i = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-clanidlist", "--clanidlist"]:
(tm_clanidListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pfamidlist", "--pfamidlist"]:
(tm_pfamidListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqid2clanid", "--seqid2clanid"]:
(seqid2clanidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqid2pfamid", "--seqid2pfamid"]:
(seqid2pfamidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pfamid2seqid", "--pfamid2seqid"]:
(pfamid2seqidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-clanid2seqid", "--clanid2seqid"]:
(clanid2seqidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pairlistwithpfamid", "--pairlistwithpfamid"]:
(pairlistwithpfamidFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-predTMdbname", "--predTMdbname"]:
(dbname_predTM, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pairlist", "--pairlist"]:
(pairListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-winsize", "--winsize"]:
(g_params['winsize'], i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-outname", "--outname"]:
(g_params['outname'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
elif argv[i] in ["-prokar", "--prokar"]:
g_params['isOnlyAnaProkar'] = True
i += 1
elif argv[i] in ["-eukar", "--eukar"]:
g_params['isOnlyAnaEukar'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
infile = argv[i]
i += 1
if myfunc.checkfile(
infile, "%s (line %d): infile" %
(__file__, inspect.currentframe().f_lineno)) != 0:
return 1
dirpath = myfunc.my_dirname(infile)
# try to obtain Pfam family tag
tag = ""
if pfamtype != "":
if pfamtype.upper().find("FAM") != -1:
tag = ".Family"
elif pfamtype.upper().find("DOM") != -1:
tag = ".Domain"
elif pfamtype.upper().find("REP") != -1:
tag = ".Repeat"
elif pfamtype.upper().find("MOT") != -1:
tag = ".Motif"
else:
tag = ""
else:
if infile.find(".Family.") != -1:
tag = ".Family"
elif infile.find(".Domain.") != -1:
tag = ".Domain"
elif infile.find(".Repeat.") != -1:
tag = ".Repeat"
elif infile.find(".Motif.") != -1:
tag = ".Motif"
else:
tag = ""
if seqid2clanidMapFile == "":
seqid2clanidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20.nr100.filter.fragmented.seqid2clanid" % (
DATADIR3)
if myfunc.checkfile(
seqid2clanidMapFile, "%s (line %d): seqid2clanidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if seqid2pfamidMapFile == "":
seqid2pfamidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20%s.nr100.filter.fragmented.seqid2pfamid" % (
DATADIR3, tag)
if myfunc.checkfile(
seqid2pfamidMapFile, "%s (line %d): seqid2pfamidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if pfamid2seqidMapFile == "":
pfamid2seqidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20.nr100.filter.fragmented.pfamid2seqid" % (
DATADIR3)
if myfunc.checkfile(
pfamid2seqidMapFile, "%s (line %d): pfamid2seqidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if clanid2seqidMapFile == "":
clanid2seqidMapFile = "%s/wk/MPTopo/pfamAna_refpro/pfammap_from_uniprot/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20%s.nr100.filter.fragmented.clanid2seqid" % (
DATADIR3, tag)
if myfunc.checkfile(
clanid2seqidMapFile, "%s (line %d): clanid2seqidMapFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if tm_pfamidListFile == "":
tm_pfamidListFile = "%s/data/pfam/pfam26.0/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20%s.pfamidlist" % (
DATADIR3, tag)
if myfunc.checkfile(
tm_pfamidListFile, "%s (line %d): tm_pfamidListFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if tm_clanidListFile == "":
tm_clanidListFile = "%s/data/pfam/pfam26.0/Pfam-A-full.seqfrompfamfasta.percentTMpro_scampi.perTM75_nseq20.clanidlist" % (
DATADIR3)
if myfunc.checkfile(
tm_clanidListFile, "%s (line %d): tm_clanidListFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if dbname_predTM == "":
dbname_predTM = "%s/wk/MPTopo/pfamAna_refpro/pred_topcons_single_method4/refpro20120604-celluar.selmaxlength-m1.topcons-single_topcons_single.m1.agree-44.RMSP" % (
DATADIR3)
if myfunc.checkfile(
"%s0.db" % (dbname_predTM), "%s (line %d): dbname_predTM" %
(__file__, inspect.currentframe().f_lineno)):
return 1
if g_params['isOnlyAnaProkar']:
prokarseqidfile = "%s/data/uniprot/reference_proteome/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.Prokaryota.seqidlist" % (
DATADIR3)
g_params['prokarSeqIDSet'] = set(myfunc.ReadIDList(prokarseqidfile))
if len(g_params['prokarSeqIDSet']) < 1:
return 1
if g_params['isOnlyAnaEukar']:
eukarseqidfile = "%s/data/uniprot/reference_proteome/refpro20120604-celluar.selmaxlength-m1.nr100.filter.fragmented.Eukaryota.seqidlist" % (
DATADIR3)
g_params['eukarSeqIDSet'] = set(myfunc.ReadIDList(eukarseqidfile))
if len(g_params['eukarSeqIDSet']) < 1:
return 1
if pairlistwithpfamidFile == "":
pairlistwithpfamidFile = "%s/../../Pfam-.maxpair100.pairlistwithpfamid" % (
dirpath)
if myfunc.checkfile(
pairlistwithpfamidFile, "%s (line %d): pairlistwithpfamidFile" %
(__file__, inspect.currentframe().f_lineno)):
return 1
pfamid_2_seqidpair_Dict = ReadPairListWithFamID(pairlistwithpfamidFile)
usedPfamIDSet = set(
pfamid_2_seqidpair_Dict.keys()) # pfamids used in pair selection
if pairListFile != "":
li = myfunc.ReadPairList(pairListFile)
SPE_PAIR_LIST = []
for tup in li:
SPE_PAIR_LIST.append((int(tup[0]), int(tup[1])))
(pfamidDefDict, clanidDefDict) = ReadPfamDefFile(pfamDefFile)
signalpDict = lcmp.ReadSignalPDict(signalpFile)
seqid2clanidDict = myfunc.ReadFam2SeqidMap(seqid2clanidMapFile)
seqid2pfamidDict = myfunc.ReadFam2SeqidMap(seqid2pfamidMapFile)
clanid2seqidDict = myfunc.ReadFam2SeqidMap(clanid2seqidMapFile)
pfamid2seqidDict = myfunc.ReadFam2SeqidMap(pfamid2seqidMapFile)
tm_pfamidList = myfunc.ReadIDList(tm_pfamidListFile)
tm_clanidList = myfunc.ReadIDList(tm_clanidListFile)
tm_pfamidSet = set(tm_pfamidList)
tm_clanidSet = set(tm_clanidList)
hdl_predTM = myfunc.MyDB(dbname_predTM)
if not hdl_predTM.failure:
idSet_TMpro = set(hdl_predTM.indexedIDList)
else:
idSet_TMpro = set([])
#classList_TableNumTMHeatMap = ["ALL", "RMSP", "RMDUP"]
#alignrangeList = ['FULL_ALIGNED', 'all', 'PART_ALIGNED']
alignrangeList = ['FULL_ALIGNED']
if g_params['outpath'] != "" and not os.path.exists(g_params['outpath']):
cmd = ["mkdir", "-p", g_params['outpath']]
try:
subprocess.check_call(cmd)
except subprocess.CalledProcessError, e:
print e
return 1
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = "./"
outfile = ""
idListFile = ""
uniprotDBname = ""
idList = []
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
idList.append(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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"]:
(idListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-uniprotdb", "--uniprotdb"]:
(uniprotDBname, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
idList.append(argv[i])
i += 1
if idListFile != "":
idList += myfunc.ReadIDList(idListFile)
if uniprotDBname == "":
print >> sys.stderr, "uniprotdb not set"
return 1
uniprotdbfile = "%s0.db" % uniprotDBname
if myfunc.checkfile(uniprotdbfile, "uniprotdbfile") != 0:
return 1
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
hdl = myfunc.MyDB(uniprotDBname)
if hdl.failure:
return 1
for seqid in idList:
data = hdl.GetRecord(seqid)
if data != None:
goinfo = GetGOInfoFromUniprotData(data)
WriteGOInfo(seqid, goinfo, fpout)
hdl.close()
myfunc.myclose(fpout)
def main(g_params):#{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
infile = ""
seqdb = ""
listfile = ""
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 ["-o", "--o", "-outfile", "--outfile"]:
outfile = argv[i+1]
i += 2
elif argv[i] in ["-i", "--i"] :
infile = argv[i+1]
i += 2
elif argv[i] in ["-l", "--l"] :
listfile = argv[i+1]
i += 2
elif argv[i] in ["-seqdb", "--seqdb"] :
seqdb = 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
runList = [] # runList is a list of tuples (infile, outfile)
if infile != "":
runList.append((infile, outfile))
if listfile != "":
if os.path.exists(listfile):
try:
fpin = open(listfile, "rU")
lines = fpin.readlines()
fpin.close()
for line in lines:
if not line or line[0]== "#":
continue
strs = line.split("\t")
infile = strs[0].strip()
try:
outfile = strs[1].strip()
except IndexError:
outfile = ""
runList.append((infile, outfile))
except IOError:
print >> sys.stderr, "Failed to read file %s"%(listfile)
else:
print >> sys.stderr, "listfile %s does not exist"%(listfile)
numInput = len(runList)
if numInput < 1:
print >> sys.stderr, "No input set. Exit"
return 1
if seqdb == "":
print >> sys.stderr, "seqdb not set."
return 1
elif not os.path.exists(seqdb+"0.db"):
print >> sys.stderr, "seqdb %s does not exist."%(seqdb)
return 1
hdl_seqdb = myfunc.MyDB(seqdb)
if hdl_seqdb.failure:
print >> sys.stderr, "Failed to open seqdb %s"%(seqdb)
return 1
for (infile, outfile) in runList:
GetSeqFromMSA(infile, outfile, hdl_seqdb)
hdl_seqdb.close()
return 0
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(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outfile = ""
outfile_tableinfo = ""
outfile_stat = ""
fileListFile = ""
fileList = []
seqdb = ""
evalue_threshold = 1e-3
coverage_threshold = 0.0
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
fileList.append(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 ["-o", "--o", "-outfile"]:
(outfile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-ot", "--ot"]:
(outfile_tableinfo, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-os", "--os"]:
(outfile_stat, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-evalue", "--evalue"]:
(evalue_threshold, i) = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-coverage", "--coverage"]:
(coverage_threshold, i) = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-seqdb", "--seqdb"]:
(seqdb, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-l", "--l"]:
(fileListFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
fileList.append(argv[i])
i += 1
if fileListFile != "":
fileList += myfunc.ReadIDList(fileListFile)
if len(fileList) < 1:
print >> sys.stderr, "No input set. exit"
return 1
if seqdb == "":
print >> sys.stderr, "Seqdb not set. exit"
return 1
hdl_seq = myfunc.MyDB(seqdb)
if hdl_seq.failure:
return 1
fpout = sys.stdout
fpout_tableinfo = None
fpout_stat = None
if outfile != "":
fpout = myfunc.myopen(outfile, sys.stdout, "w", False)
if outfile_tableinfo != "":
fpout_tableinfo = myfunc.myopen(outfile_tableinfo, None, "w", False)
if outfile_stat != "":
fpout_stat = myfunc.myopen(outfile_stat, None, "w", False)
if fpout_stat != None:
fpout_stat.write("%-8s %-8s %7s %8s %6s %6s %6s %9s %4s %9s %4s\n" % (
"#ID1",
"ID2",
"Evalue",
"Coverage",
"IDT",
"Prob",
"AlnCol",
"PosQuery",
"LenQ",
"PosTemp",
"LenT",
))
if fpout_tableinfo != None:
fpout_tableinfo.write(
"#%-15s %-15s %6s %6s %9s %6s %6s %9s %6s %6s %6s %6s %6s\n" %
("Seq1", "Seq2", "IDT0", "SIM0", "AlnLength", "Len1", "Len2",
"Score", "N_IDT", "N_SIM", "N_GAP", "IDT1", "IDT2"))
for infile in fileList:
HHAlign2Pairaln(infile, evalue_threshold, coverage_threshold, hdl_seq,
fpout, fpout_tableinfo, fpout_stat)
if outfile != "":
myfunc.myclose(fpout)
if outfile_tableinfo != "":
myfunc.myclose(fpout_tableinfo)
if outfile_stat != "":
myfunc.myclose(fpout_stat)
try:
subprocess.check_call(["mkdir", "-p", tmpdir])
except subprocess.CalledProcessError, e:
return 1
# famid2seqidDict = myfunc.ReadFam2SeqidMap(mapfile)
g_params['cdhit_wordsize'] = GetCDHitWordSize(g_params['nrlevel'])
seqdbDict = None
hdl_seqdb = None
if g_params['isBigmem']:
seqdbDict = ReadSeqDBDict(seqdb)
else:
hdl_seqdb = myfunc.MyDB(seqdb)
if hdl_seqdb.failure:
print >> sys.stderr, "Failed to load seqdb %s. exit" % (seqdb)
return 1
pfamidList = []
extra_desp_dict = {}
if extra_description_file != "":
hdl_extra = myfunc.ReadLineByBlock(extra_description_file)
if hdl_extra.failure:
print >> sys.stderr, "Failed to read extra_description_file %s." % (
extra_description_file)
return 1
lines = hdl_extra.readlines()
while lines != None:
def main(g_params): #{{{
argv = sys.argv
numArgv = len(argv)
if numArgv < 2:
PrintHelp()
return 1
outpath = ""
pairListFile = ""
seqlenFile = ""
shortid2fullidFile = ""
seqid2pfamidMapFile = ""
pfamDefFile = '/data3/data/pfam/pfam27.0/Pfam-A.clans.tsv'
topodb = ""
seqdb = ""
pdb2spFile = ""
i = 1
isNonOptionArg = False
while i < numArgv:
if isNonOptionArg == True:
isNonOptionArg = False
i += 1
return 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 ["-outpath", "--outpath"]:
(outpath, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-topodb", "--topodb"]:
(topodb, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pdb2sp", "-pdb2sp", "-pdbtosp", "--pdbtosp"]:
(pdb2spFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqdb", "--seqdb"]:
(seqdb, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seqmsapath", "--seqmsapath"]:
(g_params['seqmsapath'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-datapath", "--datapath"]:
(g_params['datapath'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-seq2pfam", "--seq2pfam"]:
(seqid2pfamidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pfam2seq", "--pfam2seq"]:
(pfamid2seqidMapFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-description", "--description"]:
(g_params['description'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pfamdef", "--pfamdef"]:
(pfamDefFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-alignrange", "--alignrange"]:
g_params['alignrange'], i = myfunc.my_getopt_str(argv, i)
if not g_params['alignrange'] in ['all', 'full', 'part']:
print >> sys.stderr, "alignrange must be one of [all, full, part]"
return 1
else:
if g_params['alignrange'] == 'full':
g_params['alignrange'] = 'FULL_ALIGNED'
elif g_params['alignrange'] == 'part':
g_params['alignrange'] = 'PART_ALIGNED'
elif argv[i] in ["-basename", "--basename"]:
(g_params['basename'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-treepath", "--treepath"]:
(g_params['treepath'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-pairalnpath", "--pairalnpath"]:
(g_params['pairalnpath'], i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-maxperfamily", "--maxperfamily"]:
(g_params['max_num_output_per_family'],
i) = myfunc.my_getopt_int(argv, i)
elif argv[i] in ["-min-seqidt", "--min-seqidt"]:
g_params['minSeqIDT'], i = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-max-seqidt", "--max-seqidt"]:
g_params['maxSeqIDT'], i = myfunc.my_getopt_float(argv, i)
elif argv[i] in ["-shortid2fullid", "--shortid2fullid"]:
(shortid2fullidFile, i) = myfunc.my_getopt_str(argv, i)
elif argv[i] in ["-debug", "--debug"]:
if argv[i + 1][0].lower() == 'y':
g_params['isDEBUG'] = True
else:
g_params['isDEBUG'] = False
i += 2
elif argv[i] in ["-q", "--q"]:
g_params['isQuiet'] = True
i += 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
else:
print >> sys.stderr, "Error! Wrong argument:", argv[i]
return 1
if g_params['basename'] == "":
print >> sys.stderr, "basename not set. exit"
return 1
if myfunc.checkfile(g_params['datapath'], "datapath") != 0:
return 1
if myfunc.checkfile(seqid2pfamidMapFile, "seqid2pfamidMapFile") != 0:
return 1
if myfunc.checkfile(pfamid2seqidMapFile, "pfamid2seqidMapFile") != 0:
return 1
if myfunc.checkfile(topodb + "0.db", "topodb") != 0:
return 1
if myfunc.checkfile(seqdb + "0.db", "seqdb") != 0:
return 1
if myfunc.checkfile(g_params['seqmsapath'], "seqmsapath") != 0:
return 1
if pdb2spFile != "":
(g_params['pdb2uniprotMap'],
g_params['uniprot2pdbMap']) = myfunc.ReadPDBTOSP(pdb2spFile)
if g_params['datapath'] == "":
print >> sys.stderr, "datapath not set"
return 1
elif not os.path.exists(g_params['datapath']):
print >> sys.stderr, "datapath %s does not exist" % (
g_params['datapath'])
return 1
if outpath == "":
print >> sys.stderr, "outpath not set"
return 1
elif not os.path.exists(outpath):
cmd = ["mkdir", "-p", outpath]
subprocess.check_call(cmd)
paircmpfile = "%s/%s.paircmp" % (g_params['datapath'],
g_params['basename'])
if myfunc.checkfile(paircmpfile, "paircmpfile") != 0:
return 1
(g_params['pfamidDefDict'],
g_params['clanidDefDict']) = lcmp.ReadPfamDefFile(pfamDefFile)
g_params['seqid2pfamidDict'] = myfunc.ReadFam2SeqidMap(seqid2pfamidMapFile)
g_params['pfamid2seqidDict'] = myfunc.ReadFam2SeqidMap(pfamid2seqidMapFile)
tmpdir = tempfile.mkdtemp()
if g_params['msapath'] == "":
g_params['msapath'] = tmpdir
if g_params['treepath'] == "":
g_params['treepath'] = tmpdir
if g_params['pairalnpath'] == "":
g_params['pairalnpath'] = tmpdir
pairCmpRecordList = []
unprocessedBuffer = ""
cntTotalReadInRecord = 0
cntTotalOutputRecord = 0
isEOFreached = False
try:
fpin = open(paircmpfile, "r")
except IOError:
print >> sys.stderr, "Failed to open input file %s" % (paircmpfile)
return 1
while 1:
buff = fpin.read(myfunc.BLOCK_SIZE)
if buff == "":
isEOFreached = True
buff = unprocessedBuffer + buff
rdList = []
unprocessedBuffer = lcmp.ReadPairCmpResultFromBuffer(buff, rdList)
rdList = FilterPairCmpResult(rdList)
cntTotalReadInRecord += len(rdList)
pairCmpRecordList += rdList
if isEOFreached == True:
break
fpin.close()
print "cntTotalReadInRecord =", cntTotalReadInRecord
g_params['hdl_seqdb'] = myfunc.MyDB(seqdb)
g_params['hdl_topodb'] = myfunc.MyDB(topodb)
g_params['OS'] = os.uname()[0]
if g_params['OS'].find('Linux') != -1:
g_params['CP_EXE'] = "/bin/cp -uf"
else:
g_params['CP_EXE'] = "/bin/cp -f"
if shortid2fullidFile != "":
g_params['uniprotAC2FullSeqIDMap'] = myfunc.ReadID2IDMap(
shortid2fullidFile)
addname = ""
if g_params['alignrange'] != 'all':
addname += ".%s" % (g_params['alignrange'])
dataTable = {}
# structure of dataTable
# dataTable[pfamid] = {'set_seqid':set(), 'difftopopair':[{'INV':[(id1,id2)]},{'TM2GAP':},{}}
# first read in pairCmpRecordList
AddAllSeqInPairCmp(dataTable, pairCmpRecordList,
g_params['seqid2pfamidDict'])
pairInfoFileList = []
for cmpclass in g_params['cmpClassList_mp3_cmpdup'][0:]:
ss = "%s/%s_.cmpdup.FULL_ALIGNED.%s.pairinfo.txt" % (
g_params['datapath'], g_params['basename'], cmpclass)
pairInfoFileList.append(ss)
pairinfoList = ReadPairInfo_cmpclass(ss)
AddPairInfo(dataTable, pairinfoList, cmpclass)
# print "\n".join(pairInfoFileList)
if g_params['isDEBUG']: #{{{
for pfamid in dataTable:
print pfamid
print "\tset_seqid"
print dataTable[pfamid]['set_seqid']
print "\tdifftopopair"
for cls in dataTable[pfamid]['difftopopair']:
print "\t\t", cls
for tup in dataTable[pfamid]['difftopopair'][cls]:
print "\t\t\t", tup #}}}
WriteHTML(dataTable, outpath)
os.system("rm -rf %s" % (tmpdir))