print line
line = infile.readline().rstrip()
coord = []
field = line.split("\t")
for item in field:
if not item == '':
coord.append(item)
locus1 = coord[0]
refCoord_start1 = int(coord[1])
refCoord_end1 = int(coord[2])
coord1_start = int(coord[3])
coord1_end = int(coord[4])
if coord1_start > coord1_end:
startingScaffold = biomodule.reverseComplement(sequences[locus1])
else:
startingScaffold = sequences[locus1]
step = 1
halfSteps = open("halpfSteps.fasta", "w")
while True:
line = infile.readline().rstrip()
if not line:
break
coord = []
field = line.split("\t")
for item in field:
if not item == '':
coord.append(item)
locus2 = coord[0]
def greedyElongation(seq):
unmappedSequences = {}
reference = str(seq)
os.system(
installationDirectory +
"src/conda/bin/cd-hit-est -d 0 -i unmapped.fasta -o unmapped_cdhit.fasta >null 2>&1"
)
cdhitfile = open("unmapped_cdhit.fasta.clstr")
#Select only high representated unmapped reads
unmapSeq = {}
for seq_record in SeqIO.parse("unmapped.fasta", "fasta"):
locus = str(seq_record.id)
if not locus in unmapSeq:
unmapSeq[locus] = str(seq_record.seq)
clusters = {}
numSeqInCluster = {}
numCluster = 0
line = cdhitfile.readline().rstrip()
if not line:
print("Do nothing")
else:
while True:
clusterName = "cluster" + str(numCluster)
if not clusterName in clusters:
clusters[clusterName] = []
numSeqInCluster[clusterName] = 0
line = "start"
while not line[0] == ">":
line = cdhitfile.readline().rstrip()
if not line:
break
numSeqInCluster["cluster" + str(numCluster)] += 1
clusters[clusterName].append(
((line.split(">"))[1].split("..."))[0])
if line[0] == ">":
numCluster += 1
if not line:
break
biggerCluster = ""
seqInBiggerScaffold = 0
for item in numSeqInCluster:
if numSeqInCluster[item] > seqInBiggerScaffold:
seqInBiggerScaffold = numSeqInCluster[item]
biggerCluster = item
print("Bigger cluster", biggerCluster, "Size", seqInBiggerScaffold)
#sys.stdin.read(1)
outcdhitfile = open("tempCdhitFile", "w")
if not len(clusters[biggerCluster]) == 0:
for sequ in clusters[biggerCluster]:
if sequ in unmapSeq:
outcdhitfile.write(">" + sequ + "\n" + unmapSeq[sequ] + "\n")
outcdhitfile.close()
os.system("mv tempCdhitFile unmapped.fasta")
for seq_record in SeqIO.parse("unmapped.fasta", "fasta"):
locus = str(seq_record.id)
if not locus in unmappedSequences:
unmappedSequences[locus] = str(seq_record.seq)
numElong = 0
while True:
toAssemble = open("toAssemble.fasta", "w")
toAssemble.write(">toElong\n" + reference[-200:] + "\n")
os.system(
installationDirectory +
"src/conda/bin/makeblastdb -in toElong.fasta -dbtype nucl >null 2>&1"
)
os.system(
installationDirectory +
"src/conda/bin/blastn -query unmapped.fasta -db toElong.fasta -outfmt 6 -num_threads 10 -dust no -soft_masking false -out outputBlast.txt >null 2>&1 "
)
blastFile = open("outputBlast.txt")
while True:
line = blastFile.readline().rstrip()
if not line:
break
fields = line.split("\t")
if (int(fields[8]) > (len(reference) - 100) or int(fields[9]) >
(len(reference) - 100)
) and abs(int(fields[9]) - int(fields[8])) > 40 and float(
fields[2]) > 95: # and fields[5] == "0":
if int(fields[8]) > int(fields[9]):
toAssemble.write(">" + fields[0] + "\n" +
biomodule.reverseComplement(
unmappedSequences[fields[0]]) + "\n")
else:
toAssemble.write(">" + fields[0] + "\n" +
unmappedSequences[fields[0]] + "\n")
toAssemble.close()
print("Perform phrap assembly step....")
os.system(installationDirectory +
"src/conda/bin/cap3 toAssemble.fasta > cap3Assembly 2>null")
numElong += 1
longestScaffold = ""
for seq_record in SeqIO.parse("toAssemble.fasta.cap.contigs", "fasta"):
if len(str(seq_record.seq)) >= len(longestScaffold):
longestScaffold = str(seq_record.seq)
#Check whether the produced elonged scaffold is on the right orientation
tempScaffold = open("tempScaffold.fasta", "w")
tempScaffold.write(">tempScaffold\n" + longestScaffold + "\n")
tempScaffold.close()
tempScaffold = open("tempScaffold_query.fasta", "w")
tempScaffold.write(">reference\n" + reference[-100:] + "\n")
tempScaffold.close()
os.system(
installationDirectory +
"src/conda/bin/makeblastdb -in tempScaffold.fasta -dbtype nucl >null 2>&1"
)
os.system(
installationDirectory +
"src/conda/bin/blastn -query tempScaffold_query.fasta -db tempScaffold.fasta -outfmt 6 -num_threads 10 -dust no -soft_masking false -out tempScaffold_outputBlast.txt >null 2>&1"
)
tempScaffold = open("tempScaffold_outputBlast.txt")
line = tempScaffold.readline().rstrip()
fieldBlast = line.split("\t")
if len(fieldBlast) > 2:
if int(fieldBlast[8]) > int(fieldBlast[9]):
longestScaffold = biomodule.reverseComplement(longestScaffold)
tempScaffold.close()
else:
print("WARNING! EXTENSION STOPPED FOR MISSING ELONGMENT!!")
js = open(
"joined_W_WARNING_" + sequenceToElong + "_" + sequenceToReach,
"w")
js.write(">joined_W_WARNING_" + sequenceToElong + "_" +
sequenceToReach + "\n" + startingSeq[:-1800] + reference)
js.close()
exit()
sc = fuseSequences2(reference, longestScaffold)
longestScaffold = sc
print("Elonged sequence has now a size of", len(longestScaffold),
"nucleotides")
if len(longestScaffold) <= len(reference):
return longestScaffold
else:
reference = longestScaffold
toElong = open("toElong.fasta", "w")
toElong.write(">toElong\n" + reference + "\n")
toElong.close()
if not line:
break
coord = []
field = line.split("\t")
for item in field:
if not item == '':
coord.append(item)
locus2 = coord[0]
coord2_start = int(coord[3])
coord2_end = int(coord[4])
tempAssembly = open("tempAssembly.fasta", 'w')
if coord2_start > coord2_end:
tempAssembly.write(">PartialGenome" + "\n" + startingScaffold + "\n" +
">" + locus2 + "\n" +
biomodule.reverseComplement(sequeunces[locus2]) +
"\n")
else:
tempAssembly.write(">PartialGenome" + "\n" + startingScaffold + "\n" +
">" + locus2 + "\n" + sequeunces[locus2] + "\n")
tempAssembly.close()
os.system("phrap tempAssembly.fasta")
numSeq = 0
for seq_record in SeqIO.parse("tempAssembly.fasta.contigs", "fasta"):
startingScaffold = str(seq_record.seq)
numSeq += 1
halfSteps.write(">" + str(step) + "\n" + startingScaffold + "\n")
if numSeq > 1:
print "More than one seq"
os.system(
installationDirectory +
"/src/conda/bin/python joinScaffolds_careful.py join ../1_cleanReads/qualityFiltered_1.fq ../1_cleanReads/qualityFiltered_2.fq finalScaffold_1_2000_f.txt r finalScaffold_"
+ str(bestPos1) + "_" + str(bestPos2) + "_r.txt r " +
installationDirectory + " 8")
for seq_record in SeqIO.parse(genomeToComplete, "fasta"):
genomeToCompleteSeq = str(seq_record.seq)
if os.path.isfile("joined_finalScaffold_1_2000_f.txt_finalScaffold_" +
bestPos1 + "_" + bestPos2 + "_r.txt") == True:
print("5' end successfully reconstructed!")
for seq_record in SeqIO.parse(
"joined_finalScaffold_1_2000_f.txt_finalScaffold_" + bestPos1 +
"_" + bestPos2 + "_r.txt", "fasta"):
firstPortion = str(seq_record.seq)
firstPortion = bm.reverseComplement(firstPortion)
firtPortionReconstructed = fuseSequences2(firstPortion,
genomeToCompleteSeq)
if len(firtPortionReconstructed) > 10:
print("firstPortion successuffly joined!")
genomeToCompleteSeq = firtPortionReconstructed
outfile = open("newGenome1.fasta", "w")
outfile.write(">finalScaffold\n" + firtPortionReconstructed + "\n")
outfile.close()
else:
print("firstPortion not joined")
outfile = open("newGenome1.fasta", "w")
outfile.write(">finalScaffold\n" + genomeToCompleteSeq + "\n")
outfile.close()
if len(longestScaffold) <= len(reference):
return longestScaffold
else:
reference = longestScaffold
toElong = open("toElong.fasta", "w")
toElong.write(">toElong\n" + reference + "\n")
toElong.close()
sequences = {}
for seq_record in SeqIO.parse(sequenceToElong, "fasta"):
startingSeq = str(seq_record.seq)
id1 = str(seq_record.id)
if sequenceToElongOrientation == "r":
startingSeq = biomodule.reverseComplement(startingSeq)
for seq_record in SeqIO.parse(sequenceToReach, "fasta"):
terminiSeq = str(seq_record.seq)
id2 = str(seq_record.id)
if sequenceToReachOrientation == "r":
terminiSeq = biomodule.reverseComplement(terminiSeq)
termfile = open("termini.fasta", "w")
termfile.write(">termini\n" + terminiSeq[:500] + "\n")
termfile.close()
toElong = open("toElong.fasta", "w")
toElong.write(">toElong\n" + startingSeq[-1800:-300] + "\n")
toElong.close()
downstreamAlignment = fields
lastNucl = int(fields[9])
if len(downstreamAlignment) > 0:
newSequence = s1[:int(downstreamAlignment[9]
)] + s2[int(downstreamAlignment[7]):]
blastFile.close()
return newSequence
else:
return ""
for seq_record in SeqIO.parse(start, "fasta"):
startSeq = str(seq_record.seq)
if start_o == "r":
startSeq = biomodule.reverseComplement(startSeq)
for seq_record in SeqIO.parse(end, "fasta"):
terminiSeq = str(seq_record.seq)
if end_o == "r":
terminiSeq = biomodule.reverseComplement(terminiSeq)
elongedSequence = startSeq[-700:-200]
outputSeq = open("joinScaffold_trivialSeq.fasta", "w")
numCycle = 0
while True:
bestElongation = 0
numCycle += 1
if numCycle == numCycles:
outputSeq.write(">trivialSeq\n" + startSeq[:-700] + elongedSequence +
"\n")
print "Lunghezza migliore Scaffold:",lengthBestScaffold
print "Overhang:",overhang
#Check forward contigs
if reference[-15:] in sequence and (len(fuseSequences(reference,sequence))-len(reference)) > overhang:
elongedSequence = fuseSequences(reference,sequence)
overhang = len(elongedSequence)-len(reference)
print "Sequence",elongedSequence
print "Forward"
print "Overhang",len(elongedSequence)-len(reference)
#print "Dove si trova la sequenza ",sequence.find(reference[-15:])
#print "Da cercare ",reference[-15:]
print seq_record
#sys.stdin.read(1)
#Check reverse contigs
revSequence = biomodule.reverseComplement(sequence)
if reference[-15:] in revSequence and (len(fuseSequences(reference,revSequence))-len(reference)) > overhang:
elongedSequence = fuseSequences(reference,revSequence)
overhang = len(elongedSequence)-len(reference)
print "Sequence",elongedSequence
print "Reverse"
print "Overhang",len(elongedSequence)-len(reference)
#print "Dove si trova la sequenza ",sequence.find(reference[-15:])
#print "Da cercare ",reference[-15:]
print seq_record
#sys.stdin.read(1)
if overhang < 10:
print "Poor elongment. Now exit...."
os.system("cp toElong.fasta elonged.fasta")
def greedyElongation(seq):
unmappedSequences = {}
reference = str(seq)
#os.system("mkdir tempor")
for seq_record in SeqIO.parse("unmapped.fasta", "fasta"):
locus = str(seq_record.id)
if not locus in unmappedSequences:
unmappedSequences[locus] = str(seq_record.seq)
numElong = 0
while True:
#print "Perform the blast of the unmapped sequences...."
toAssemble = open("toAssemble.fasta", "w")
toAssemble.write(">toElong\n" + reference[-200:] + "\n")
os.system(
installationDirectory +
"src/conda/bin/makeblastdb -in toElong.fasta -dbtype nucl >null 2>&1"
)
os.system(
installationDirectory +
"src/conda/bin/blastn -query unmapped.fasta -db toElong.fasta -outfmt 6 -num_threads 8 -dust no -soft_masking false -out outputBlast.txt >null 2>&1"
)
#print "Done"
#print "Fill the toAssemble file"
blastFile = open("outputBlast.txt")
while True:
line = blastFile.readline().rstrip()
if not line:
break
fields = line.split("\t")
if (int(fields[8]) > (len(reference) - 100) or int(fields[9]) >
(len(reference) - 100)
) and abs(int(fields[9]) - int(fields[8])) > 40 and float(
fields[2]) > 97 and fields[5] == "0":
if int(fields[8]) > int(fields[9]):
toAssemble.write(">" + fields[0] + "\n" +
biomodule.reverseComplement(
unmappedSequences[fields[0]]) + "\n")
else:
toAssemble.write(">" + fields[0] + "\n" +
unmappedSequences[fields[0]] + "\n")
toAssemble.close()
print("Perform second phrap assembly step.......")
os.system(installationDirectory +
"src/conda/bin/cap3 toAssemble.fasta > cap3Assembly 2>null")
numElong += 1
longestScaffold = ""
for seq_record in SeqIO.parse("toAssemble.fasta.cap.contigs", "fasta"):
if len(str(seq_record.seq)) >= len(longestScaffold):
longestScaffold = str(seq_record.seq)
#Check whether the produced elonged scaffold is on the right orientation
tempScaffold = open("tempScaffold.fasta", "w")
tempScaffold.write(">tempScaffold\n" + longestScaffold + "\n")
tempScaffold.close()
tempScaffold = open("tempScaffold_query.fasta", "w")
tempScaffold.write(">reference\n" + reference[-100:] + "\n")
tempScaffold.close()
os.system(
installationDirectory +
"src/conda/bin/makeblastdb -in tempScaffold.fasta -dbtype nucl >null 2>&1"
)
os.system(
installationDirectory +
"src/conda/bin/blastn -query tempScaffold_query.fasta -db tempScaffold.fasta -outfmt 6 -num_threads 10 -dust no -soft_masking false -out tempScaffold_outputBlast.txt >null 2>&1"
)
tempScaffold = open("tempScaffold_outputBlast.txt")
line = tempScaffold.readline().rstrip()
fieldBlast = line.split("\t")
if len(fieldBlast) > 2:
if int(fieldBlast[8]) > int(fieldBlast[9]):
longestScaffold = biomodule.reverseComplement(longestScaffold)
tempScaffold.close()
else:
print("WARNING! EXTENSION STOPPED!!")
js = open(
"joined_W_WARNING_" + sequenceToElong + "_" + sequenceToReach,
"w")
js.write(">joined_W_WARNING_" + sequenceToElong + "_" +
sequenceToReach + "\n" + startingSeq[:-1800] + reference)
js.close()
exit()
sc = fuseSequences2(reference, longestScaffold)
longestScaffold = sc
print("Elonged sequence has now a size of", len(longestScaffold),
"nucleotides")
if len(longestScaffold) <= len(reference):
return longestScaffold
else:
reference = longestScaffold
toElong = open("toElong.fasta", "w")
toElong.write(">toElong\n" + reference + "\n")
toElong.close()
for seq_record in SeqIO.parse(
outputFolder + "/" + sampleName + "/hcmv_genome.fasta_con.fasta",
"fasta"):
consensusSequence = str(seq_record.seq)
else:
for seq_record in SeqIO.parse(consensusFile, "fasta"):
consensusSequence = str(seq_record.seq)
#**************************************************************************************************************
#Create file with repeat flanking regions fro consensus sequence (this is needed by pipeline step 2)***********
flankingSequencesFile = open("repeatsFlanking.fasta", "w")
flankingSequencesFile.write(
">TRLflankingStarting\n" +
bm.reverseComplement(consensusSequence[1364:3000]) + "\n")
flankingSequencesFile.write(
">TRLflankingEnding\nCCATTCCGGGCCGTGTGCTGGGTCCCCGAGGGGCGGGGGGGTGTTTTCTGCGGGGGGGTGAAATTTGGAGTTGCGTGTGTGGACGGCGACGGCGACTAGTTGCGTGTGCTGCGGTGGGTACGGCGACGGCGAATAAAAGCGACGTGCGGCGCGCACGGCGAAAAGCAGACGCGCGTCTGTGTCTGTTTGAGTCCCCAGGGGACGGCAGCG\n"
)
flankingSequencesFile.write(">IRflankingStarting\n" +
consensusSequence[192000:193500] + "\n")
flankingSequencesFile.write(">IRflankingEnding\n" +
consensusSequence[197000:197500] + "\n")
flankingSequencesFile.write(">TRSflankingEnding\n" +
consensusSequence[232000:233500] + "\n")
flankingSequencesFile.write(
">TRLflankingEnding\nCCCGGCCAACACACCCCGACACACCCGGCACACGCCCGCGACACACCCGGCCAACACACCCCGACACACCCGGCACACGCCCGCGACACACCCGCGGCACACCCTGACACACCCGCCACACCCGGCACACACCCACCCCGCCGCGCCCCCGACACACCCCGACCGCCGCCGGTGCGGGACAGGGCT\n"
)
flankingSequencesFile.close()
os.system("mv repeatsFlanking.fasta ./2_ElongationFlankingRepeats/")
#****************************************************************************************************************
sequence[startPosition:]), len(reference), str(
seq_record.id)
if reference[:20] in sequence:
if len(sequence) > lengthBestScaffold:
lengthBestScaffold = len(sequence)
startPosition = sequence.find(reference[:20])
elongedSequence = sequence[startPosition:]
bestScaffold = sequence
overhang = len(sequence[startPosition:]) - len(reference)
print "Overhang composition:", len(
sequence[startPosition:]), len(reference), str(
seq_record.id)
#check reverse contigs
if biomodule.reverseComplement(reference[:20]) in sequence:
if len(sequence) > lengthBestScaffold:
lengthBestScaffold = len(sequence)
startPosition = (biomodule.reverseComplement(sequence)).find(
reference[:20])
elongedSequence = (
biomodule.reverseComplement(sequence))[startPosition:]
bestScaffold = sequence
overhang = len((biomodule.reverseComplement(sequence)
)[startPosition:]) - len(reference)
print "Overhang composition:", len(
(biomodule.reverseComplement(sequence)
)[startPosition:]), len(reference), str(seq_record.id)
if overhang < 10:
print "Poor elongment. Now exit...."
