biorseo.py
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#!/usr/bin/python3
# coding=utf-8
import getopt, multiprocessing, subprocess, sys
import matplotlib.pyplot as plt
from scipy import stats
from os import path, makedirs, getcwd, chdir, devnull, remove, walk
from matplotlib import colors
from math import sqrt
from multiprocessing import cpu_count, Manager
from shutil import move
from ast import literal_eval
# Parse options
try:
cmd_opts, cmd_args = getopt.getopt( sys.argv[1:],
"bc:f:hi:jl:no:O:pt:v",
[ "verbose","rna3dmotifs","3dmotifatlas","carnaval","contacts","jar3d","bayespairing","patternmatch","func=",
"help","version","seq=","modules-path=", "jar3d-exec=", "bypdir=", "biorseo-dir=", "first-objective=","output=","theta=",
"interrupt-limit=", "outputf="])
except getopt.GetoptError as err:
print(err)
sys.exit(2)
m = Manager()
running_stats = m.list()
running_stats.append(0) # n_launched
running_stats.append(0) # n_finished
running_stats.append(0) # n_skipped
ignored_nt_dict = {}
def is_canonical_nts(seq):
"""Checks if a nucleotide is ACGU, and stores it in a dictionnary if it's not,
with an occurrence count."""
for c in seq[:-1]:
if c not in "ACGU":
if c in ignored_nt_dict.keys():
ignored_nt_dict[c] += 1
else:
ignored_nt_dict[c] = 1
return False
return True
def absolutize_path(p, directory=False):
if p[0] != '/':
p = getcwd() + '/' + p
if directory and p[-1] != '/':
p = p + '/'
return p
class NoDaemonProcess(multiprocessing.Process):
@property
def daemon(self):
return False
@daemon.setter
def daemon(self, value):
pass
class NoDaemonContext(type(multiprocessing.get_context())):
Process = NoDaemonProcess
class MyPool(multiprocessing.pool.Pool):
# We sub-class multiprocessing.pool.Pool instead of multiprocessing.Pool
# because the latter is only a wrapper function, not a proper class.
def __init__(self, *args, **kwargs):
kwargs['context'] = NoDaemonContext()
super(MyPool, self).__init__(*args, **kwargs)
class Loop:
"""Just a data structure to store module informations."""
def __init__(self, header, subsequence, looptype, position):
self.header = header
self.seq = subsequence
self.type = looptype
self.position = position
class InsertionSite:
"""An interval of an RNA sequence where a particular module could be inserted.
The philosophy of Biorseo is : if this portion can fold like this module,
then it may be a loop of the corresponding type."""
def __init__(self, loop, csv_line):
# BEWARE : jar3d csv output is crap because of java's locale settings.
# On french OSes, it uses commas to delimit the fields AND as floating point delimiters !!
# Parse with caution, and check what the csv output files look like on your system...
info = csv_line.split(',')
self.loop = loop # the Loop object that has been searched with jar3d
# position of the loop's components, so the motif's ones, in the query sequence.
self.position = loop.position
# Motif model identifier of the RNA 3D Motif Atlas
self.atlas_id = info[2]
# alignment score of the subsequence to the motif model
self.score = int(float(info[4]))
# should the motif model be inverted to fit the sequence ?
self.rotation = int(info[-2])
def __lt__(self, other):
"""compare two insertion sites scores"""
return self.score < other.score
def __gt__(self, other):
"""compare two insertion sites scores"""
return self.score > other.score
class Job:
"""A class to store the properties of a tool execution, in order to run similar jobs in parallel."""
def __init__(self, command=None, function=None, args=None, how_many_in_parallel=0, priority=1, timeout=None):
self.cmd_ = command
self.func_ = function
self.args_ = args
self.priority_ = priority
self.timeout_ = timeout
if not how_many_in_parallel:
self.nthreads = cpu_count()
elif how_many_in_parallel == -1:
self.nthreads = cpu_count() - 1
else:
self.nthreads = how_many_in_parallel
class RNA:
"""Just a data structure gathering header, sequence and length."""
def __init__(self, header, seq):
self.seq_ = seq
self.header = header
self.length = len(seq)
class BiorseoInstance:
"""A run of the biorseo tool, to predict one or several RNA sequences' folding(s),
including all the necessary previous run of other tools."""
def __init__(self, opts):
# set default run type options
self.type = "dpm" # direct pattern mathcing
self.modules = "desc" # ...with Rna3dMotifs "DESC" modules
self.func = 'B' # ...and function B
self.forward_options = [] # options to pass to the C++ biorseo
self.jobcount = 0
self.joblist = []
# set default file output locations
self.finalname = ""
self.outputf = "" # A folder where to output the computation files
if path.exists("/biorseo/results"): # docker image default
self.outputf = "/biorseo/results"
self.output = "" # A file to store the solutions
# set default data input locations
self.mode = 0 # default is single sequence mode
self.inputfile = ""
self.jar3d_exec = "/jar3d_2014-12-11.jar"
self.bypdir = "/byp/src" # Docker image locations
self.HL_motif_dir = "/modules/BGSU/HL/3.2/lib"
self.IL_motif_dir = "/modules/BGSU/IL/3.2/lib"
self.desc_folder = "/modules/DESC"
self.rin_folder = "/modules/RIN/Subfiles"
self.json_folder = "/modules/ISAURE"
self.biorseo_dir = "/biorseo"
self.run_dir = path.dirname(path.realpath(__file__))
self.temp_dir = "temp/"
for opt, arg in opts:
if opt == "-h" or opt == "--help":
print( "Biorseo, Bi-Objective RNA Structure Efficient Optimizer\n"
"Bio-objective integer linear programming framework to predict RNA secondary structures by including known RNA modules.\n"
"Developped by Louis Becquey (louis.becquey@univ-evry.fr), 2018-2020\n\n")
print("Usage:\tYou must provide:\n\t1) a FASTA input file with -i,\n\t2) a module type with --rna3dmotifs, --carnaval, --contacts or --3dmotifatlas"
"\n\t3) one module placement method in { --patternmatch, --jar3d, --bayespairing }\n\t4) one scoring function with --func A, B, C or D"
"\n\n\tIf you are not using the Docker image: \n\t5) --modules-path, --biorseo-dir and (--jar3d-exec or --bypdir)")
print()
print("Options:")
print("-h [ --help ]\t\t\tPrint this help message")
print("--version\t\t\tPrint the program version")
print("-i [ --seq=… ]\t\t\tFASTA file with the query RNA sequence")
print("--rna3dmotifs\t\t\tUse DESC modules from Djelloul & Denise, 2008")
print("--carnaval\t\t\tUse RIN modules from Reinharz & al, 2018")
print("--3dmotifatlas\t\t\tUse the HL and IL loops from BGSU's 3D Motif Atlas (updated)")
print("--contacts\t\t\tUse .json motif from Isaure")
print("-p [ --patternmatch ]\t\tUse regular expressions to place modules in the sequence (requires --rna3dmotifs or --carnaval)")
print("-j [ --jar3d ]\t\t\tUse JAR3D to place modules in the sequence (requires --3dmotifatlas)")
print("-b [ --bayespairing ]\t\tUse BayesPairing2 to place modules in the sequence (requires --rna3dmotifs or --3dmotifatlas)")
print("-o [ --output=… ]\t\tFile to summarize the results")
print("-O [ --outputf=… ]\t\tFolder where to output result and temp files")
print("-f [ --func=… ]\t\t\t(A, B, C or D, default is B)"
" Objective function to score module insertions:\n\t\t\t\t (A) insert big modules (B) insert light, high-order modules"
"\n\t\t\t\t (c) insert modules which score well with the sequence\n\t\t\t\t (D) insert light, high-order modules which score well with the sequence."
"\n\t\t\t\t C and D require cannot be used with --patternmatch.")
print("-c [ --first-objective=… ]\t(default 1) Objective to solve in the mono-objective portions of the algorithm."
"\n\t\t\t\t (1) is the module objective given by --func, (2) is the expected accuracy of the structure.")
print("-l [ --limit=… ]\t\t(default 500) Number of solutions in the Pareto set from which"
"\n\t\t\t\t we give up the computation, before eliminating secondary structure doublons.")
print("-t [ --theta=… ]\t\t(default 0.001) Pairing-probability threshold to consider or not the possibility of pairing")
print("-n [ --disable-pseudoknots ]\tAdd constraints to explicitly forbid the formation of pseudoknots")
print("-v [ --verbose ]\t\tPrint what is happening to stdout")
print("--modules-path=…\t\tPath to the modules data.\n\t\t\t\t The folder should contain modules in the DESC format as output by Djelloul & Denise's"
"\n\t\t\t\t 'catalog' program for use with --rna3dmotifs, or the IL/ and HL/ folders\n\t\t\t\t from a release of the RNA 3D Motif Atlas "
"for use with --3dmotifatlas, or the\n\t\t\t\t data/modules/RIN/Subfiles/ folder for use with --carnaval.\n\t\t\t\t Consider placing these files on a fast I/O device (NVMe SSD, ...)")
print("--jar3d-exec=…\t\t\tPath to the jar3d executable.\n\t\t\t\t Default is /jar3d_2014-12-11.jar, you should use this option if you run"
"\n\t\t\t\t BiORSEO from outside the docker image.")
print("--bypdir=…\t\t\tPath to the BayesParing src folder.\n\t\t\t\t Default is /byp/src, you should use this option if you run"
"\n\t\t\t\t BiORSEO from outside the docker image.")
print("--biorseo-dir=…\t\t\tPath to the BiORSEO root directory.\n\t\t\t\t Default is /biorseo, you should use this option if you run"
"\n\t\t\t\t BiORSEO from outside the docker image. Use the FULL path.")
print("\nExamples:")
print("biorseo.py -i myRNA.fa -O myResultsFolder/ --rna3dmotifs --patternmatch --func B")
print("biorseo.py -i myRNA.fa -O myResultsFolder/ --3dmotifatlas --jar3d --func B -l 800")
print("biorseo.py -i myRNA.fa -v --3dmotifatlas --bayespairing --func D")
print("\nThe allowed module/placement-method/function combinations are:\n")
print(" --patternmatch --bayespairing --jar3d")
print("--rna3dmotifs A. B. A. B. C. D.")
print("--3dmotifatlas A. B. C. D. A. B. C. D.")
print("--carnaval A. B.")
print("--contacts A. B. E. D.\n")
sys.exit()
elif opt == "-i" or opt == "--seq":
self.inputfile = arg
elif opt == "-O" or opt == "--outputf":
self.outputf = absolutize_path(arg, directory=True) # output folder
elif opt == "-o" or opt == "--output":
self.output = absolutize_path(arg) # output file
elif opt == "-f" or opt == "--func":
if arg in ['A', 'B', 'C', 'D', 'E', 'F']:
self.func = arg
else:
raise "Unknown scoring function " + arg
elif opt == "-p" or opt == "--patternmatch":
self.type = "dpm"
elif opt == "-j" or opt == "--jar3d":
self.type = "jar3d"
elif opt == "-b" or opt == "--bayespairing":
self.type = "byp"
elif opt == "--carnaval":
self.modules = "rin"
elif opt == "--contacts":
self.modules = "json"
elif opt == "--rna3dmotifs":
self.modules = "desc"
elif opt == "--3dmotifatlas":
self.modules = "bgsu"
elif opt == "--modules-path":
self.HL_motif_dir = absolutize_path(arg, directory=True) + "HL/3.2/lib"
self.IL_motif_dir = absolutize_path(arg, directory=True) + "IL/3.2/lib"
self.desc_folder = absolutize_path(arg, directory=True)
self.rin_folder = absolutize_path(arg, directory=True)
self.json_folder = absolutize_path(arg, directory=True)
print("Looking for modules in", arg)
elif opt == "--jar3d-exec":
self.jar3d_exec = absolutize_path(arg)
print("Using ", arg)
elif opt == "--bypdir":
self.bypdir = absolutize_path(arg, directory=True)
print("Using trained BayesPairing in", arg)
elif opt == "--biorseo-dir":
self.biorseo_dir = absolutize_path(arg, directory=True)
elif opt == "--version":
subprocess.run([self.biorseo_dir+"bin/biorseo", "--version"])
exit(0)
elif opt == "-l" or opt == "--interrupt-limit":
self.forward_options.append("-l")
self.forward_options.append(arg)
elif opt == "-v" or opt == "--verbose":
self.forward_options.append("-v")
elif opt == "-n" or opt == "--disable-pseudoknots":
self.forward_options.append("-n")
elif opt == "-t" or opt == "--theta":
self.forward_options.append("-t")
self.forward_options.append(arg)
elif opt == "-c" or opt == "--first-objective":
self.forward_options.append("-c")
self.forward_options.append(arg)
# Check the argument combination is OK
self.check_args()
if self.outputf != "":
print("saving files to", self.outputf)
# create jobs
self.list_jobs()
# run them
self.execute_jobs()
# locate the results at the right place
if self.output != "":
subprocess.run(["mv", self.temp_dir+self.finalname.split('/')[-1], self.output], check=True)
if self.outputf != "":
for src_dir, _, files in walk(self.temp_dir):
dst_dir = src_dir.replace(self.temp_dir, self.outputf, 1)
if not path.exists(dst_dir):
makedirs(dst_dir)
for file_ in files:
src_file = path.join(src_dir, file_)
dst_file = path.join(dst_dir, file_)
if path.exists(dst_file):
# in case of the src and dst are the same file
if path.samefile(src_file, dst_file):
continue
remove(dst_file)
move(src_file, dst_dir)
subprocess.run(["rm", "-rf", self.temp_dir], check=True) # remove the temp folder
def check_args(self):
"""Checks that the argument combination passed by user is a realistic project"""
warning = "ERROR: The argument list you passed contains errors:"
issues = False
if self.modules == "desc" and self.type == "jar3d":
issues = True
print(warning)
print("/!\\ Using jar3d requires the 3D Motif Atlas modules. Use --3dmotifatlas instead of --rna3dmotifs or --carnaval.")
if (self.modules == "desc" or self.modules == "rin" or self.modules == "bgsu") and (self.func == 'E' or self.func == 'F'):
issues = True
print(warning)
print("/!\\ Functions E and F are only compatible with the contacts library from Isaure.")
if self.modules == "rin" and self.type != "dpm":
issues = True
print(warning)
print("/!\\ CaRNAval does not support placement tools (yet), or scoring tools. Please use it with --patternmatch, not --jar3d nor --bayespairing.")
if self.modules == "json" and (self.type != "dpm" or self.func == 'C' or self.func == 'D'):
issues = True
print(warning)
print("/!\\ Contacts does not support placement tools (yet). Please use it with --patternmatch, not --jar3d nor --bayespairing.")
if self.modules == "bgsu" and self.type == "dpm":
issues = True
print(warning)
print("/!\\ Cannot place the Atlas loops by direct pattern matching. Please use a dedicated tool --jar3d or --bayespairing to do so.")
if issues:
print("\nUsage:\tYou must provide:\n\t1) a FASTA input file with -i,\n\t2) one module type in { --rna3dmotifs, --carnaval, --3dmotifatlas, --contacts }"
"\n\t3) one module placement method in { --patternmatch, --jar3d, --bayespairing }\n\t4) one scoring function with --func A, B, C or D"
"\n\n\tIf you are not using the Docker image: \n\t5) --modules-path, --biorseo-dir and (--jar3d-exec or --bypdir)")
print("\nThe allowed module/placement-method/function combinations are:\n")
print(" --patternmatch --bayespairing --jar3d")
print("--rna3dmotifs A. B. A. B. C. D.")
print("--3dmotifatlas A. B. C. D. A. B. C. D.")
print("--carnaval A. B.")
print("--contacts A. B. E. F.\n")
exit(1)
def enumerate_loops(self, s):
"""Lists all the loop positions in a dot-bracket notation"""
def resort(unclosedLoops):
loops.insert(len(loops)-1-unclosedLoops, loops[-1])
loops.pop(-1)
opened = []
openingStart = []
closingStart = []
loops = []
loopsUnclosed = 0
consecutiveOpenings = []
if s[0] == '(':
consecutiveOpenings.append(1)
consecutiveClosings = 0
lastclosed = -1
previous = ''
for i in range(len(s)):
# If we arrive on an unpaired segment
if s[i] == '.':
if previous == '(':
openingStart.append(i-1)
if previous == ')':
closingStart.append(i-1)
# Opening basepair
if s[i] == '(':
if previous == '(':
consecutiveOpenings[-1] += 1
else:
consecutiveOpenings.append(1)
if previous == ')':
closingStart.append(i-1)
# We have something like (...(
if len(openingStart) and openingStart[-1] == opened[-1]:
# Create a new loop starting with this component.
loops.append([(openingStart[-1], i)])
openingStart.pop(-1)
loopsUnclosed += 1
# We have something like )...( or even )(
if len(closingStart) and closingStart[-1] == lastclosed:
# Append a component to existing multiloop
loops[-1].append((closingStart[-1], i))
closingStart.pop(-1)
opened.append(i)
# Closing basepair
if s[i] == ')':
if previous == ')':
consecutiveClosings += 1
else:
consecutiveClosings = 1
# This is not supposed to happen in real data, but whatever.
if previous == '(':
openingStart.append(i-1)
# We have something like (...) or ()
if len(openingStart) and openingStart[-1] == opened[-1]:
# Create a new loop, and save it as already closed (HL)
loops.append([(openingStart[-1], i)])
openingStart.pop(-1)
resort(loopsUnclosed)
# We have something like )...)
if len(closingStart) and closingStart[-1] == lastclosed:
# Append a component to existing multiloop and close it.
loops[-1].append((closingStart[-1], i))
closingStart.pop(-1)
loopsUnclosed -= 1
resort(loopsUnclosed)
if i+1 < len(s):
if s[i+1] != ')': # We are on something like: ).
# an openingStart has not been correctly detected, like in ...((((((...)))...)))
if consecutiveClosings < consecutiveOpenings[-1]:
# Create a new loop (uncompleted)
loops.append([(opened[-2], opened[-1])])
loopsUnclosed += 1
# We just completed an HL+stem, like ...(((...))).., we can forget its info
if consecutiveClosings == consecutiveOpenings[-1]:
consecutiveClosings = 0
consecutiveOpenings.pop(-1)
else: # There are still several basepairs to remember, forget only the processed ones, keep the others
consecutiveOpenings[-1] -= consecutiveClosings
consecutiveClosings = 0
else: # We are on something like: ))
# we are on an closingStart that cannot be correctly detected, like in ...(((...(((...))))))
if consecutiveClosings == consecutiveOpenings[-1]:
# Append a component to the uncomplete loop and close it.
loops[-1].append((i, i+1))
loopsUnclosed -= 1
resort(loopsUnclosed)
# Forget the info about the processed stem.
consecutiveClosings = 0
consecutiveOpenings.pop(-1)
opened.pop(-1)
lastclosed = i
previous = s[i]
# print(i,"=",s[i],"\t", "consec. Op=", consecutiveOpenings,"Cl=",consecutiveClosings)
return loops
def launch_JAR3D_worker(self, loop):
"""Launches a jar3d search of specific loop types (IL or HL) on a RNA subsequence (fasta file)"""
# write motif to a file
modulefolder = self.temp_dir + loop.header[1:] + '/'
if not path.exists(modulefolder):
makedirs(modulefolder)
filename = modulefolder + loop.header[1:]+".fasta"
fasta = open(filename, 'w')
fasta.write('>'+loop.header+'\n'+loop.seq+'\n')
fasta.close()
# Launch Jar3D on it
if loop.type == 'h':
cmd = ["java", "-jar", self.jar3d_exec, loop.header[1:]+".fasta", self.HL_motif_dir+"/all.txt",
loop.header[1:]+".HLloop.csv", loop.header[1:]+".HLseq.csv"]
else:
cmd = ["java", "-jar", self.jar3d_exec, loop.header[1:]+".fasta", self.IL_motif_dir+"/all.txt",
loop.header[1:]+".ILloop.csv", loop.header[1:]+".ILseq.csv"]
with open(self.temp_dir + "log_of_the_run.sh", 'a') as logfile:
logfile.write(' '.join(cmd) + '\n')
chdir(modulefolder)
with open(devnull, 'w') as nowhere:
subprocess.run(cmd, stdout=nowhere)
chdir(self.biorseo_dir)
# Retrieve results
insertion_sites = []
if loop.type == 'h':
capstype = "HL"
else:
capstype = "IL"
csv = open(modulefolder + loop.header[1:] +".%sseq.csv" % capstype, 'r')
l = csv.readline()
while l:
if "true" in l:
insertion_sites.append(InsertionSite(loop, l))
l = csv.readline()
csv.close()
return insertion_sites
def launch_JAR3D(self, seq_, basename):
"""Identify loops in a RNA sequence from RNAsubopt results and search
for 3D motif Atlas modules to place on it using jar3d."""
rnasubopt_preds = []
# Extracting probable loops from RNA-subopt structures
rna = open(self.temp_dir + basename + ".subopt", "r")
lines = rna.readlines()
rna.close()
for i in range(2, len(lines)):
ss = lines[i].split(' ')[0]
if ss not in rnasubopt_preds:
rnasubopt_preds.append(ss)
HLs = []
ILs = []
for ss in rnasubopt_preds:
loop_candidates = self.enumerate_loops(ss)
for loop_candidate in loop_candidates:
if len(loop_candidate) == 1 and loop_candidate not in HLs:
HLs.append(loop_candidate)
if len(loop_candidate) == 2 and loop_candidate not in ILs:
ILs.append(loop_candidate)
# 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))
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))
# 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 ]
pool.close()
pool.join()
insertion_sites.sort(reverse=True)
# Writing results to CSV file
c = 0
resultsfile = open(self.biorseo_dir + "/" + self.temp_dir+basename+".sites.csv", "w")
resultsfile.write("Motif,Rotation,Score,Start1,End1,Start2,End2\n")
for site in insertion_sites:
if site.score > 10:
c += 1
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.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]
if len(positions) == 1:
positions.append("-,-")
resultsfile.write(','.join(positions)+'\n')
resultsfile.close()
def launch_BayesPairing(self, module_type, seq_, header_):
"""DEPRECATED: now we are using Bayespairing 2.
Searches for module occurrences in the provided RNA sequence using BayesPairing 1."""
# Run BayePairing
cmd = ["python3", "parse_sequences.py", "-seq", self.biorseo_dir + '/' + self.temp_dir + header_ + ".fa", "-d", module_type, "-interm", "1"]
logfile = open(self.biorseo_dir + "/" + self.temp_dir + "log_of_the_run.sh", 'a')
logfile.write(" ".join(cmd))
logfile.write("\n")
logfile.close()
chdir(self.bypdir)
out = subprocess.check_output(cmd).decode('utf-8')
BypLog = out.split('\n')
# Extract results from command output to file
idx = 0
l = BypLog[idx]
while l[:3] != "PUR":
idx += 1
l = BypLog[idx]
insertion_sites = [x for x in literal_eval(l.split(":")[1][1:])]
if module_type == "rna3dmotif":
rna = open(self.biorseo_dir + "/" + self.temp_dir + header_ + ".byp.csv", "w")
else:
rna = open(self.biorseo_dir + "/" + self.temp_dir + header_ + ".bgsubyp.csv", "w")
rna.write("Motif,Score,Start1,End1,Start2,End2...\n")
for i, module in enumerate(insertion_sites):
if len(module):
for (score, positions, _) in zip(*[iter(module)]*3):
pos = []
q = -2
for p in positions:
if p-q > 1:
pos.append(q)
pos.append(p)
q = p
pos.append(q)
rna.write(module_type+str(i)+','+str(int(score)))
for (p, q) in zip(*[iter(pos[1:])]*2):
if q > p:
rna.write(','+str(p)+','+str(q))
rna.write('\n')
rna.close()
def launch_BayesPairing2(self, module_type, seq_, header_):
"""Search for module occurrences in the provided RNA sequence using BayesPairing 2"""
# Run BayesPairing 2
if module_type=="rna3dmotif":
BP2_type = "rna3dmotif"
else:
BP2_type = "3dMotifAtlas_ALL"
cmd = ["python3", "parse_sequences.py", "-seq", self.biorseo_dir + '/' + self.temp_dir + header_ + ".fa", "-samplesize", "1000", "-d", BP2_type ]
logfile = open(self.temp_dir + "log_of_the_run.sh", 'a')
logfile.write(" ".join(cmd))
logfile.write("\n")
logfile.close()
chdir(self.bypdir)
out = subprocess.check_output(cmd).decode('utf-8')
Byp2Log = out.splitlines()
# remove what is not in the original input
Byp2Log.pop(0)
Byp2Log.pop(0)
Byp2Log.pop()
Byp2Log.pop()
# remove the 2 first lines of output
Byp2Log.pop(0)
Byp2Log.pop(0)
# Extract results from command line output to file
lines = []
for i in range(len(Byp2Log)):
line = Byp2Log[i].replace("|", ' ').replace(",", ' ').split()
if line != []:
if "=" in line[0]: #skip the "| MODULE N HITS PERCENTAGE |" part
break
module_sequence = line.pop().split("&") #remove the sequence
if line != []:
new_line = [line[0], line[1]]
num_comp = 0
position_index = 2
while num_comp < len(module_sequence):
len_comp = 0
comp = module_sequence[num_comp]
element = line[position_index].split("-")
new_line.append(element[0])
if position_index >= len(line):
print("!!! Skipped one BP2 result : positions not matching sequence length\n")
new_line = []
break
while len_comp < len(comp):
element = line[position_index].split("-")
if len(element)==1:
len_comp += 1
else:
len_comp += int(element[1]) - int(element[0]) + 1
position_index += 1
new_line.append(element[-1])
num_comp += 1
if new_line != [] :
lines.append(new_line)
if module_type=="rna3dmotif":
rna = open(self.biorseo_dir + "/" + self.temp_dir + header_ + ".byp2.csv", "w")
else:
rna = open(self.biorseo_dir + "/" + self.temp_dir + header_ + ".bgsubyp2.csv", "w")
rna.write("Motif,Score,Start1,End1,Start2,End2...\n")
for line in lines:
rna.write(module_type)
for i in range(len(line)-1):
rna.write(line[i] + ",")
rna.write(line[-1] + "\n")
rna.close()
def execute_job(self, j):
"""Execute the command or function stored in a Job class object."""
running_stats[0] += 1
if j.cmd_ is not None:
logfile = open(self.biorseo_dir + "/" + self.temp_dir + "log_of_the_run.sh", 'a')
logfile.write(" ".join(j.cmd_))
logfile.write("\n")
logfile.close()
print("["+str(running_stats[0]+running_stats[2]) +
'/'+str(self.jobcount)+"]\t"+" ".join(j.cmd_))
r = subprocess.run(j.cmd_, timeout=j.timeout_)
elif j.func_ is not None:
print("["+str(running_stats[0]+running_stats[2])+'/'+str(self.jobcount) +
"]\t"+j.func_.__name__+'('+", ".join([a for a in j.args_])+')')
try:
if j.args_ is not None:
r = j.func_(*j.args_)
else:
r = j.func_()
except Exception as e:
r = 1
print("\033[31m", e, "\033[0m")
pass
running_stats[1] += 1
return r
def execute_jobs(self):
"""Groups job by priority and ability to be run in parallel,
and runs them."""
jobs = {}
self.jobcount = len(self.joblist)
for job in self.joblist:
if job.priority_ not in jobs.keys():
jobs[job.priority_] = {}
if job.nthreads not in jobs[job.priority_].keys():
jobs[job.priority_][job.nthreads] = []
jobs[job.priority_][job.nthreads].append(job)
nprio = max(jobs.keys())
if len(jobs) > 1 :
for i in range(1,nprio+1):
if not len(jobs[i].keys()): continue
# check the thread numbers
different_thread_numbers = [ n for n in jobs[i].keys() ]
different_thread_numbers.sort()
for n in different_thread_numbers:
bunch = jobs[i][n]
if not len(bunch): continue
pool = MyPool(processes=n)
pool.map(self.execute_job, bunch)
pool.close()
pool.join()
else:
for job in self.joblist:
self.execute_job(job)
def list_jobs(self):
"""Determines the required tool runs we need before running the C++ Biorseo,
and creates a job list to run."""
if self.outputf != "":
subprocess.run(["mkdir", "-p", self.outputf]) # Create the output folder
subprocess.run(["mkdir", "-p", self.temp_dir]) # Create the temp folder
# Read fasta file, which can contain one or several RNAs
RNAcontainer = []
print("loading file %s..." % self.inputfile)
db = open(self.inputfile, "r")
c = 0
header = ""
seq = ""
while True:
l = db.readline()
if l == "":
break
c += 1
c = c % 2
if c == 1:
if header != "": # This is our second RNA in the fasta file
self.mode = 1 # we switch to batch mode
header = l[1:-1]
if c == 0:
seq = l.upper()
if is_canonical_nts(seq):
header = header.replace('/', '_').replace('\'','').replace('(','').replace(')','').replace(' ','_').replace('>','')
if (header != ""):
RNAcontainer.append(RNA(header, seq))
if not path.isfile(self.temp_dir + header + ".fa"):
rna = open(self.temp_dir + header + ".fa", "w")
rna.write(">" + header +'\n')
rna.write(seq +'\n')
rna.close()
db.close()
for nt, number in ignored_nt_dict.items():
print("ignored %d sequences because of char %c" % (number, nt))
tot = len(RNAcontainer)
print("Loaded %d RNAs." % (tot))
# define job list
for instance in RNAcontainer:
executable = self.biorseo_dir + "bin/biorseo"
fastafile = self.temp_dir+instance.header+".fa"
method_type = ""
priority = 1
if self.type == "jar3d":
ext = ".jar3d"
method_type = "--jar3dcsv"
csv = self.temp_dir + 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.temp_dir], 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
if self.type == "byp":
method_type = "--bayespaircsv"
if self.modules == "desc":
ext = ".byp2"
csv = self.temp_dir + instance.header + ".byp2.csv"
self.joblist.append(Job(function=self.launch_BayesPairing2, args=["rna3dmotif", instance.seq_, instance.header], how_many_in_parallel=1, priority=1))
elif self.modules == "bgsu":
ext = ".bgsubyp2"
csv = self.temp_dir + instance.header + ".bgsubyp2.csv"
self.joblist.append(Job(function=self.launch_BayesPairing2, args=["3dmotifatlas", instance.seq_, instance.header], how_many_in_parallel=1, priority=1))
priority = 2
if self.type == "dpm":
if self.modules == "desc":
method_type = "--descfolder"
csv = self.desc_folder
ext = ".desc_pm"
elif self.modules == "rin":
method_type = "--rinfolder"
csv = self.rin_folder
ext = ".rin_pm"
elif self.modules == "json":
method_type = "--jsonfolder"
csv = self.json_folder
ext = ".json_pm"
command = [ executable, "-s", fastafile ]
if method_type:
command += [ method_type, csv ]
self.finalname = self.temp_dir + instance.header + ext + self.func
command += [ "-o", self.finalname, "--function", self.func ]
command += self.forward_options
self.joblist.append(Job(command=command, priority=priority, timeout=3600, how_many_in_parallel=3))
BiorseoInstance(cmd_opts)