def prepareNextBatch(self):
self.nextBatchX = np.zeros(
(self.batchSize, self.numKds, self.numTFs)) + np.log(99999.0)
self.nextBatchY = np.zeros((self.batchSize))
b = 0
while b < self.batchSize:
line = self.curFH.readline()
if line == "":
if self.numRuns == 1:
self.nextBatchX = self.nextBatchX[0:b, :, :]
self.nextBatchY = self.nextBatchY[0:b]
self.numRuns -= 1
return
self.curFH.close()
self.curFH = MYUTILS.smartGZOpen(self.inFP, 'r')
self.numRuns -= 1
line = self.curFH.readline()
if line is None or line[0] == "#": continue
curData = line.split("\t")
self.nextBatchY[b] = float(curData[0])
for t in range(1, len(curData)):
curKds = [np.log(float(x)) for x in curData[t].split(";")]
self.nextBatchX[b, 0:min(self.numKds, len(curKds)), t -
1] = curKds[0:min(self.numKds, len(curKds))]
b += 1
def makeBowtieDB():
global args
## Uses global keyword to access variables defined outside the function.
global promoterSeqs
fastaOut = MYUTILS.smartGZOpen(args.tempFilePre + ".seqs.fasta", 'w')
## Define the output FASTA file.
for i in range(0, len(promoterSeqs)):
fastaOut.write(">%i\n%s\n" % (i, promoterSeqs[i]))
## Prints the promoter seqs in FASTA format:
## >1
## ATCGATCGATCGTCAGTAGCTCGTACGTAGCGACTGCTCGTAGC...
## >2
## ATCGATCGCTACGATGCTAGATGCTCGATCGTCGTACGTACGTA...
fastaOut.close()
## Close the file.
#subprocess.check_call(["bowtie2-build","%s.seqs.fasta"%args.tempFilePre,"%s.bowtie2"%args.tempFilePre], stdout=subprocess.PIPE, stdin=subprocess.PIPE);
p = subprocess.Popen(
["bowtie2-build"] + args.bowtieBuildParams.split() +
["%s.seqs.fasta" % args.tempFilePre,
"%s.bowtie2" % args.tempFilePre],
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.PIPE)
if args.verbose > 0:
sys.stderr.write("Running bowtie2-build...")
(curStdout, stderrData) = p.communicate()
## Popen.communicate interact with process:
## Send data to stdin. Read data from stdout and stderr,
## until end-of-file is reached.
if args.verbose > 0:
sys.stderr.write(curStdout)
sys.stderr.write(stderrData)
sys.stderr.write("done!\n")
def prepareNextBatch(self):
self.nextBatchX = np.zeros(
(self.batchSize, self.seqLen - self.wordLen + 1)).astype("int32")
self.nextBatchY = np.zeros((self.batchSize))
b = 0
while b < self.batchSize:
line = self.curFH.readline()
if line == "":
if self.numRuns == 1:
self.nextBatchX = self.nextBatchX[0:b, :, :]
self.nextBatchY = self.nextBatchY[0:b]
self.numRuns -= 1
return
self.curFH.close()
self.curFH = MYUTILS.smartGZOpen(self.inFP, 'r')
self.numRuns -= 1
line = self.curFH.readline()
if line is None or line[0] == "#": continue
curData = line.rstrip().split("\t")
self.nextBatchY[b] = float(curData[0])
curSeq = curData[1]
if len(curSeq) < self.seqLen:
curSeq = "N" * (self.seqLen - len(curSeq)) + curSeq
### prepend Ns if the sequence is too short
curSeq = curSeq[(
len(curSeq) -
self.seqLen):len(curSeq)] # trim distal bases if too long
for si in range(0, self.seqLen - self.wordLen + 1):
self.nextBatchX[b, si] = self.kmer2index[curSeq[si:(
si + self.wordLen
)]] #fill X with the indeces of the various k-mers
b += 1
def __init__(self, inFP, batchSize, numRuns, seqLen):
self.inFP = inFP
self.batchSize = batchSize
self.numRuns = numRuns
self.seqLen = seqLen
self.curFH = MYUTILS.smartGZOpen(self.inFP, 'r')
self.curThread = Thread(target=self.prepareNextBatch)
self.curThread.start()
def saveMatrix(outFileName, rowLabs, colLabs, dataMatrix):
outFile = MYUTILS.smartGZOpen(outFileName, "w")
outFile.write("\t".join(colLabs) + "\n")
for i in range(0, len(rowLabs)):
outFile.write(rowLabs[i])
for j in range(0, dataMatrix.shape[1]):
outFile.write("\t%g" % dataMatrix[i, j])
outFile.write("\n")
outFile.close()
def __init__(self, inFP, batchSize, numRuns,numTFs, numKds): self.inFP = inFP; self.batchSize = batchSize; self.numRuns= numRuns; self.numTFs= numTFs; self.numKds= numKds; self.curFH = MYUTILS.smartGZOpen(self.inFP,'r') self.curThread = Thread(target = self.prepareNextBatch); self.curThread.start()
def __init__(self, inFP, batchSize, numRuns,seqLen, kmer2index, wordLen): self.inFP = inFP; self.batchSize = batchSize; self.numRuns= numRuns; self.seqLen= seqLen; self.wordLen= wordLen; self.kmer2index= kmer2index; self.curFH = MYUTILS.smartGZOpen(self.inFP,'r') self.curThread = Thread(target = self.prepareNextBatch); self.curThread.start()
def prepareNextBatch(self):
self.nextBatchX = np.zeros((self.batchSize, 4, self.seqLen, 1))
self.nextBatchY = np.zeros((self.batchSize))
b = 0
while b < self.batchSize:
line = self.curFH.readline()
if line == "":
if self.numRuns == 1:
self.nextBatchX = self.nextBatchX[0:b, :, :, :]
self.nextBatchY = self.nextBatchY[0:b]
self.numRuns -= 1
return
self.curFH.close()
self.curFH = MYUTILS.smartGZOpen(self.inFP, 'r')
self.numRuns -= 1
line = self.curFH.readline()
if line is None or line[0] == "#": continue
curData = np.fromstring(line, dtype=float, sep="\t")
self.nextBatchY[b] = curData[0]
self.nextBatchX[b, :, :, 0] = curData[1:].reshape((4, self.seqLen))
b += 1
def prepareNextBatch(self): self.nextBatchX = np.zeros((self.batchSize,self.numKds,self.numTFs)) +np.log(99999.0); self.nextBatchY = np.zeros((self.batchSize)) b=0 while b < self.batchSize: line = self.curFH.readline() if line =="": if self.numRuns==1: self.nextBatchX = self.nextBatchX[0:b,:,:] self.nextBatchY = self.nextBatchY[0:b] self.numRuns-=1; return; self.curFH.close(); self.curFH = MYUTILS.smartGZOpen(self.inFP,'r') self.numRuns-=1; line = self.curFH.readline() if line is None or line[0]=="#": continue curData = np.fromstring(line, dtype=float, sep="\t") self.nextBatchY[b]=curData[0]; self.nextBatchX[b,:,:] = np.transpose(curData[1:len(curData)].reshape((self.numTFs,self.numKds))) b+=1
def makeBowtieDB():
global args
global promoterSeqs
fastaOut = MYUTILS.smartGZOpen(args.tempFilePre + ".seqs.fasta", 'w')
for i in range(0, len(promoterSeqs)):
fastaOut.write(">%i\n%s\n" % (i, promoterSeqs[i]))
fastaOut.close()
#subprocess.check_call(["bowtie2-build","%s.seqs.fasta"%args.tempFilePre,"%s.bowtie2"%args.tempFilePre], stdout=subprocess.PIPE, stdin=subprocess.PIPE);
p = subprocess.Popen(
["bowtie2-build"] + args.bowtieBuildParams.split() +
["%s.seqs.fasta" % args.tempFilePre,
"%s.bowtie2" % args.tempFilePre],
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.PIPE)
if args.verbose > 0:
sys.stderr.write("Running bowtie2-build...")
(curStdout, stderrData) = p.communicate()
if args.verbose > 0:
sys.stderr.write(curStdout)
sys.stderr.write(stderrData)
sys.stderr.write("done!\n")
required=False)
parser.add_argument('-l',
dest='logFP',
metavar='<logFile>',
help='Where to output errors/warnings [default=stderr]',
required=False)
parser.add_argument('-v',
dest='verbose',
action='count',
help='Verbose output?',
required=False,
default=0)
args = parser.parse_args()
inFileDict = MYUTILS.smartGZOpen(args.inFPDict, 'r')
inFileSeqs = MYUTILS.smartGZOpen(args.inFPSeqs, 'r')
if (args.logFP is not None):
logFile = MYUTILS.smartGZOpen(args.logFP, 'w')
sys.stderr = logFile
if (args.outFP is None):
outFile = sys.stdout
else:
if args.verbose > 0:
sys.stderr.write("Outputting to file " + args.outFP + "\n")
outFile = MYUTILS.smartGZOpen(args.outFP, 'w')
translationDict = {}
#raise Exception("Reached bad state=%d for '%s.%d' '%s' at line '%s'" %(state,mid,ver,tfid,line));
required=False)
parser.add_argument('-l',
dest='logFP',
metavar='<logFile>',
help='Where to output errors/warnings [default=stderr]',
required=False)
parser.add_argument('-v',
dest='verbose',
action='count',
help='Verbose output?',
required=False,
default=0)
args = parser.parse_args()
inFile1 = MYUTILS.smartGZOpen(args.inFP1, 'r')
inFile2 = MYUTILS.smartGZOpen(args.inFP2, 'r')
if (args.logFP is not None):
logFile = MYUTILS.smartGZOpen(args.logFP, 'w')
sys.stderr = logFile
if (args.outFP is None):
outFile = sys.stdout
else:
if args.verbose > 0: warnings.warn("Outputting to file " + args.outFP)
outFile = MYUTILS.smartGZOpen(args.outFP, 'w')
def getNextRead(inFile):
name = inFile.readline().rstrip()
## Can execute 'python seqToOHC.py --help' from command line to see options.
## Supporting information at https://docs.python.org/3/library/argparse.html
parser = argparse.ArgumentParser(description='Converts a set of sequences into a one-hot-code (binary) representation - excludes non [ATGC] chars. Output in ACGT order, one line per sequence, base then position.');
parser.add_argument('-i',dest='inFP', metavar='<inFile>', help='Input file of sequences with a value in the second column that will preceed the OHC output on each line, separated by a tab', required=True);
parser.add_argument('-m',dest='maxLen', metavar='<maxSeqLen>',help='The maximum sequence length to consider (truncated after this point)', required=True);
parser.add_argument('-b',dest='orientBack', action='count',help='Align sequences of different sizes to back [default=front]?', required=False, default=0);
parser.add_argument('-o',dest='outFP', metavar='<outFile>',help='Where to output results [default=stdout]', required=False);
parser.add_argument('-l',dest='logFP', metavar='<logFile>',help='Where to output errors/warnings [default=stderr]', required=False);
parser.add_argument('-v',dest='verbose', action='count',help='Verbose output?', required=False, default=0);
## initialize parser
args = parser.parse_args();
## Uses the smartGZOpen function in MYUTILS to read/parse through a file
## (indicated by 'r' argument).
inFile=MYUTILS.smartGZOpen(args.inFP,'r');
## Initialize max length integer
maxSeqLen = int(args.maxLen);
## Creates log file of errors/warnings
## logFile = flexible framework to emit log messages
## (logging = tracking events when software runs)
if (args.logFP is not None):
logFile=MYUTILS.smartGZOpen(args.logFP,'w');
sys.stderr=logFile;
## Creates output directions (inculding warnings)
if (args.outFP is None):
## system specific function - standard output, if output
outFile= sys.stdout;
else:
dest='skipAlignment',
action='count',
help=
'Skip the alignment step (e.g. was already done)? - also skip DB creation',
required=False,
default=0)
args = parser.parse_args()
## The variable 'verbose' is an integer with the value given above, where the '-v'
## argument is added.
verbose = args.verbose
## Creates a log file of errors/warnings (as described above)
if (args.logFP is not None):
logFile = MYUTILS.smartGZOpen(args.logFP, 'w')
sys.stderr = logFile
#test if bowtie exists
## 'subprocess' spawns new process. Here the call is 'which bowtie'. If the call is successful, the returncode (and
## therefore the value of p) is 0. Otherwise, the returncode will be non-zero, and an Exception is raised.
p = subprocess.call(["which", "bowtie2"],
stdin=subprocess.PIPE,
stderr=subprocess.PIPE)
if p != 0:
raise Exception("could not find bowtie2. Did you use Bowtie2 ?")
## Uses the smartGZOpen function in MYUTILS to write (indicated by 'w' argument) a file.
## File has name with the prefix passed by user using the '-o' flag, and will have
## suffix as indicated in the arguments.
outFileMap = MYUTILS.smartGZOpen(args.outFPre + "_map.txt.gz", 'w')
