Louis BECQUEY / biorseo

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Louis BECQUEY
1c59c960 1 parent 72060257

some cleaning + temp folder

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Showing 1 changed file with 35 additions and 250 deletions
......@@ -25,6 +25,7 @@ modulespath = biorseoDir + "/data/modules"
HLmotifDir = modulespath + "/BGSU/HL/3.2/lib"
ILmotifDir = modulespath + "/BGSU/IL/3.2/lib"
descfolder = modulespath + "/DESC"
tempDir = "temp/"
# Parse options
try:
......@@ -84,12 +85,6 @@ class Loop:
self.type = looptype
self.position = position
def get_header(self):
return self.header
def subsequence(self):
return self.seq
class InsertionSite:
def __init__(self, loop, csv_line):
......@@ -151,177 +146,6 @@ class RNA:
self.biorseoBGSUBayesPairD = []
self.biorseoBGSUBayesPairB = []
def get_RNAsubopt_results(self):
rna = open(self.outputf + self.basename + ".subopt", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0]
if ss not in self.rnasubopt.predictions:
self.rnasubopt.predictions.append(ss)
def get_biorseoBayesPairA_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bypA"):
rna = open(targetdir+ self.basename + ".bypA", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBayesPairA.predictions:
self.biorseoBayesPairA.predictions.append(ss)
self.biorseoBayesPairA.ninsertions.append(lines[i].count('+'))
def get_biorseoBayesPairB_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bypB"):
rna = open(targetdir+ self.basename + ".bypB", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBayesPairB.predictions:
self.biorseoBayesPairB.predictions.append(ss)
self.biorseoBayesPairB.ninsertions.append(lines[i].count('+'))
def get_biorseoBayesPairC_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bypC"):
rna = open(targetdir+ self.basename + ".bypC", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBayesPairC.predictions:
self.biorseoBayesPairC.predictions.append(ss)
self.biorseoBayesPairC.ninsertions.append(lines[i].count('+'))
def get_biorseoBayesPairD_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bypD"):
rna = open(targetdir+ self.basename + ".bypD", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBayesPairD.predictions:
self.biorseoBayesPairD.predictions.append(ss)
self.biorseoBayesPairD.ninsertions.append(lines[i].count('+'))
def get_biorseoRawA_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".rawA"):
rna = open(targetdir+ self.basename + ".rawA", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoRawA.predictions:
self.biorseoRawA.predictions.append(ss)
self.biorseoRawA.ninsertions.append(lines[i].count('+'))
def get_biorseoRawB_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".rawB"):
rna = open(targetdir+ self.basename + ".rawB", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoRawB.predictions:
self.biorseoRawB.predictions.append(ss)
self.biorseoRawB.ninsertions.append(lines[i].count('+'))
def get_biorseoBGSUJAR3DA_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".jar3dA"):
rna = open(targetdir+ self.basename + ".jar3dA", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUJAR3DA.predictions:
self.biorseoBGSUJAR3DA.predictions.append(ss)
self.biorseoBGSUJAR3DA.ninsertions.append(lines[i].count('+'))
def get_biorseoBGSUJAR3DB_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".jar3dB"):
rna = open(targetdir+ self.basename + ".jar3dB", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUJAR3DB.predictions:
self.biorseoBGSUJAR3DB.predictions.append(ss)
self.biorseoBGSUJAR3DB.ninsertions.append(lines[i].count('+'))
def get_biorseoBGSUJAR3DC_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".jar3dC"):
rna = open(targetdir+ self.basename + ".jar3dC", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUJAR3DC.predictions:
self.biorseoBGSUJAR3DC.predictions.append(ss)
self.biorseoBGSUJAR3DC.ninsertions.append(lines[i].count('+'))
def get_biorseoBGSUJAR3DD_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".jar3dD"):
rna = open(targetdir+ self.basename + ".jar3dD", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUJAR3DD.predictions:
self.biorseoBGSUJAR3DD.predictions.append(ss)
self.biorseoBGSUJAR3DD.ninsertions.append(lines[i].count('+'))
def get_biorseoBGSUBayesPairA_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bgsubypA"):
rna = open(targetdir+ self.basename + ".bgsubypA", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUBayesPairA.predictions:
self.biorseoBGSUBayesPairA.predictions.append(ss)
self.biorseoBGSUBayesPairA.ninsertions.append(lines[i].count('+'))
# else:
# print(targetdir+ self.basename + ".bgsubypA not found !")
def get_biorseoBGSUBayesPairB_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bgsubypB"):
rna = open(targetdir+ self.basename + ".bgsubypB", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUBayesPairB.predictions:
self.biorseoBGSUBayesPairB.predictions.append(ss)
self.biorseoBGSUBayesPairB.ninsertions.append(lines[i].count('+'))
# else:
# print(targetdir+ self.basename + ".bgsubypB not found !")
def get_biorseoBGSUBayesPairC_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bgsubypC"):
rna = open(targetdir+ self.basename + ".bgsubypC", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUBayesPairC.predictions:
self.biorseoBGSUBayesPairC.predictions.append(ss)
self.biorseoBGSUBayesPairC.ninsertions.append(lines[i].count('+'))
# else:
# print(targetdir+ self.basename + ".bgsubypC not found !")
def get_biorseoBGSUBayesPairD_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bgsubypD"):
rna = open(targetdir+ self.basename + ".bgsubypD", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0].split('\t')[0]
if ss not in self.biorseoBGSUBayesPairD.predictions:
self.biorseoBGSUBayesPairD.predictions.append(ss)
self.biorseoBGSUBayesPairD.ninsertions.append(lines[i].count('+'))
# else:
# print(targetdir+ self.basename + ".bgsubypD not found !")
class BiorseoInstance:
def __init__(self, opts):
......@@ -420,7 +244,9 @@ class BiorseoInstance:
self.list_jobs()
# run them
self.execute_jobs()
self.execute_jobs()
# subprocess.call(["rm", "-rf", tempDir]) # empty the temp folder
def enumerate_loops(self, s):
def resort(unclosedLoops):
......@@ -532,28 +358,29 @@ class BiorseoInstance:
def launch_JAR3D_worker(self, loop):
# write motif to a file
newpath = getcwd()+'/'+loop.header[1:]
if not path.exists(newpath):
makedirs(newpath)
chdir(newpath)
filename = loop.header[1:]+".fasta"
modulefolder = tempDir + loop.header[1:] + '/'
if not path.exists(modulefolder):
makedirs(modulefolder)
filename = modulefolder + loop.header[1:]+".fasta"
fasta = open(filename, 'w')
fasta.write('>'+loop.get_header()+'\n'+loop.subsequence()+'\n')
fasta.write('>'+loop.header+'\n'+loop.seq+'\n')
fasta.close()
# Launch Jar3D on it
if loop.type == 'h':
cmd = ["java", "-jar", jar3dexec, filename, HLmotifDir+"/all.txt",
cmd = ["java", "-jar", jar3dexec, loop.header[1:]+".fasta", HLmotifDir+"/all.txt",
loop.header[1:]+".HLloop.csv", loop.header[1:]+".HLseq.csv"]
else:
cmd = ["java", "-jar", jar3dexec, filename, ILmotifDir+"/all.txt",
cmd = ["java", "-jar", jar3dexec, loop.header[1:]+".fasta", ILmotifDir+"/all.txt",
loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"]
nowhere = open(devnull, 'w')
logfile = open(biorseoDir + "/log_of_the_run.sh", 'a')
logfile.write(' '.join(cmd))
logfile.write("\n")
logfile.close()
chdir(modulefolder)
subprocess.call(cmd, stdout=nowhere)
chdir(biorseoDir)
nowhere.close()
# Retrieve results
......@@ -562,7 +389,7 @@ class BiorseoInstance:
capstype = "HL"
else:
capstype = "IL"
csv = open(loop.header[1:]+".%sseq.csv" % capstype, 'r')
csv = open(modulefolder + loop.header[1:] +".%sseq.csv" % capstype, 'r')
l = csv.readline()
while l:
if "true" in l:
......@@ -570,15 +397,12 @@ class BiorseoInstance:
l = csv.readline()
csv.close()
# Cleaning
chdir("..")
subprocess.call(["rm", "-r", loop.header[1:]])
return insertion_sites
def launch_JAR3D(self, seq_, basename):
rnasubopt_preds = []
# Extracting probable loops from RNA-subopt structures
rna = open(self.outputf + basename + ".subopt", "r")
rna = open(tempDir + basename + ".subopt", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
......@@ -597,19 +421,16 @@ class BiorseoInstance:
# Retrieve subsequences corresponding to the possible loops
loops = []
for i, l in enumerate(HLs):
loops.append(
Loop(">HL%d" % (i+1), seq_[l[0][0]-1:l[0][1]], "h", l))
loops.append(Loop(">HL%d" % (i+1), seq_[l[0][0]-1:l[0][1]], "h", l))
for i, l in enumerate(ILs):
loops.append(
Loop(">IL%d" % (i+1), seq_[l[0][0]-1:l[0][1]]+'*'+seq_[l[1][0]-1:l[1][1]], "i", l))
loops.append(Loop(">IL%d" % (i+1), seq_[l[0][0]-1:l[0][1]]+'*'+seq_[l[1][0]-1:l[1][1]], "i", l))
# Scanning loop subsequences against motif database
pool = MyPool(processes=cpu_count())
insertion_sites = [x for y in pool.map(
self.launch_JAR3D_worker, loops) for x in y]
insertion_sites = [x for y in pool.map(self.launch_JAR3D_worker, loops) for x in y]
insertion_sites.sort(reverse=True)
# Writing results to CSV file
c = 0
resultsfile = open(self.outputf+basename+".sites.csv", "w")
resultsfile = open(biorseoDir + "/" + tempDir+basename+".sites.csv", "w")
resultsfile.write("Motif,Rotation,Score,Start1,End1,Start2,End2\n")
for site in insertion_sites:
if site.score > 10:
......@@ -617,7 +438,7 @@ class BiorseoInstance:
string = "FOUND with score %d:\t\t possible insertion of motif " % site.score + site.atlas_id
if site.rotation:
string += " (reversed)"
string += (" on " + site.loop.get_header() + " at positions")
string += (" on " + site.loop.header + " at positions")
resultsfile.write(site.atlas_id+',' +
str(bool(site.rotation))+",%d" % site.score+',')
positions = [','.join([str(y) for y in x]) for x in site.position]
......@@ -629,10 +450,10 @@ class BiorseoInstance:
def launch_BayesPairing(self, module_type, seq_, header_):
chdir(bypdir)
cmd = ["python3", "parse_sequences.py", "-seq", self.outputf +
cmd = ["python3", "parse_sequences.py", "-seq", biorseoDir + '/' + tempDir +
header_ + ".fa", "-d", module_type, "-interm", "1"]
logfile = open("log_of_the_run.sh", 'a')
logfile = open(biorseoDir + "/log_of_the_run.sh", 'a')
logfile.write(" ".join(cmd))
logfile.write("\n")
logfile.close()
......@@ -646,9 +467,9 @@ class BiorseoInstance:
l = BypLog[idx]
insertion_sites = [x for x in ast.literal_eval(l.split(":")[1][1:])]
if module_type == "rna3dmotif":
rna = open(self.outputf + header_ + ".byp.csv", "w")
rna = open(biorseoDir + "/" + tempDir + header_ + ".byp.csv", "w")
else:
rna = open(self.outputf + header_ + ".bgsubyp.csv", "w")
rna = open(biorseoDir + "/" + tempDir + header_ + ".bgsubyp.csv", "w")
rna.write("Motif,Score,Start1,End1,Start2,End2...\n")
for i, module in enumerate(insertion_sites):
if len(module):
......@@ -687,8 +508,8 @@ class BiorseoInstance:
except:
r = 1
pass
if r:
fails.append(j)
# if r:
# fails.append(j)
running_stats[1] += 1
return r
......@@ -729,48 +550,12 @@ class BiorseoInstance:
print("Computations ran successfully.")
print()
def check_result_existence(self, datatype, method, function, with_PK, basename):
folder = self.outputf+"PK/" if with_PK else self.outputf+"noPK/"
if datatype == "bgsu":
if method == "jar3d":
extension = ".jar3d"
elif method == "byp":
extension = ".bgsubyp"
else:
raise "Unknown method !"
elif datatype == "desc":
if method == "dpm":
extension = ".raw"
elif method == "byp":
extension = ".byp"
else:
raise "Unknown method !"
else:
raise "Unknown data type !"
return path.isfile(folder + basename + extension + function)
def check_csv_existence(self, datatype, method, basename):
if datatype == "bgsu":
if method == "jar3d":
extension = ".sites.csv"
elif method == "byp":
extension = ".bgsubyp.csv"
else:
raise "Unknown method !"
elif datatype == "desc":
if method == "byp":
extension = ".byp.csv"
else:
raise "You cannot use " + method + " with " + datatype + " data !"
else:
raise "Unknown data type !"
return path.isfile(self.outputf + basename + extension)
def list_jobs(self):
# Read fasta file, which can contain one or several RNAs
RNAcontainer = []
subprocess.call(["mkdir", "-p", self.outputf]) # Create the output folder
subprocess.call(["mkdir", "-p", tempDir]) # Create the temp folder
print("loading file %s..." % self.inputfile)
db = open(self.inputfile, "r")
c = 0
......@@ -789,10 +574,10 @@ class BiorseoInstance:
if c == 0:
seq = l[:-1].upper()
if is_canonical_nts(seq):
header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','').replace(' ','_')
header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','').replace(' ','_').replace('>','')
RNAcontainer.append(RNA(header, seq))
if not path.isfile(self.outputf + header + ".fa"):
rna = open(self.outputf + header + ".fa", "w")
if not path.isfile(tempDir + header + ".fa"):
rna = open(tempDir + header + ".fa", "w")
rna.write(">" + header +'\n')
rna.write(seq +'\n')
rna.close()
......@@ -807,7 +592,7 @@ class BiorseoInstance:
for instance in RNAcontainer:
executable = biorseoDir + "/bin/biorseo"
fastafile = self.outputf+instance.header+".fa"
fastafile = tempDir+instance.header+".fa"
method_type = ""
ext = ".raw"
priority = 1
......@@ -815,11 +600,11 @@ class BiorseoInstance:
if self.type == "jar3d":
ext = ".jar3d"
method_type = "--jar3dcsv"
csv = self.outputf + instance.header + ".sites.csv"
csv = tempDir + instance.header + ".sites.csv"
# RNAsubopt
self.joblist.append(Job(command=["RNAsubopt", "-i", fastafile, "--outfile="+ instance.header + ".subopt"], priority=1))
self.joblist.append(Job(command=["mv", instance.header + ".subopt", self.outputf], priority=2))
self.joblist.append(Job(command=["mv", instance.header + ".subopt", tempDir], priority=2))
# JAR3D
self.joblist.append(Job(function=self.launch_JAR3D, args=[instance.seq_, instance.header], priority=3, how_many_in_parallel=1))
priority = 4
......@@ -827,11 +612,11 @@ class BiorseoInstance:
method_type = "--bayespaircsv"
if self.modules == "desc":
ext = ".byp"
csv = self.outputf + instance.header + ".byp.csv"
csv = tempDir + instance.header + ".byp.csv"
self.joblist.append(Job(function=self.launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header], how_many_in_parallel=-1, priority=1))
elif self.modules == "bgsu":
ext = ".bgsubyp"
csv = self.outputf + instance.header + ".bgsubyp.csv"
csv = tempDir + instance.header + ".bgsubyp.csv"
self.joblist.append(Job(function=self.launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header], how_many_in_parallel=-1, priority=1))
priority = 2
if self.type == "dpm":
......