Louis BECQUEY / biorseo

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Louis BECQUEY
41896738 1 parent e3bb834e

-O option to keep temp files

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Showing 2 changed files with 63 additions and 17 deletions
......@@ -43,7 +43,11 @@ OBJECTIVE FUNCTIONS FOR THE MODULE INSERTION CRITERIA
* **Function C** : weights a module by its insertion site score (JAR3D or BayesPairing score).
* **Function D** : weights a module by its number of components (strands) and insertion site score (JAR3D or BayesPairing score), and penalizes it by the log^(_2) of its nucleotide size.
3/ Recommended uses
3/ Installation
==================================
Check the file INSTALL.md for installation instructions.
4/ Recommended uses
==================================
- If **you know you have no pseudoknot**:
* Benchmarks show Biorseo does not perform better than simpler tools like RNAsubopt alone. Please use RNAsubopt (ViennaRNA package) or Fold (RNAstructure package).
......@@ -55,11 +59,6 @@ OBJECTIVE FUNCTIONS FOR THE MODULE INSERTION CRITERIA
* The use of the RNA 3D Motif Atlas placed by JAR3D and scored with function B is not subject to combinatorial issues, but performs a bit worse. It also returns less solutions. Example:
`./bin/biorseo -i PDB_00304.fa --3dmotifatlas --jar3d --func B`
4/ Installation
==================================
Check the file INSTALL.md for installation instructions.
5/ List of Options
==================================
```
......@@ -69,7 +68,8 @@ Check the file INSTALL.md for installation instructions.
-p [ --patternmatch ] Use regular expressions to place modules in the sequence
-j [ --jar3d ] Use JAR3D to place modules in the sequence (requires --3dmotifatlas)
-b [ --bayespairing ] Use BayesPairing to place modules in the sequence
-o [ --output=… ] Folder where to output files
-o [ --output=… ] File to summarize the results
-O [ --outputf=… ] Folder where to output result and temp files
-f [ --func=… ] (A, B, C or D, default is B) Objective function to score module insertions:
(A) insert big modules (B) insert light, high-order modules
(c) insert modules which score well with the sequence
......
......@@ -4,13 +4,14 @@ import sys
import getopt
from scipy import stats
import subprocess
from os import path, makedirs, getcwd, chdir, devnull
from os import path, makedirs, getcwd, chdir, devnull, remove, walk
import matplotlib.pyplot as plt
from matplotlib import colors
from math import sqrt
from multiprocessing import cpu_count, Manager
import multiprocessing
import ast
from shutil import move
# ================== DEFINITION OF THE PATHS ==============================
......@@ -29,7 +30,9 @@ tempDir = "temp/"
# Parse options
try:
opts, args = getopt.getopt(sys.argv[1:], "bc:f:hi:jl:no:pt:v", ["verbose", "rna3dmotifs","3dmotifatlas","jar3d","bayespairing","patternmatch","func=","help","version","seq=","modules-path=", "first-objective=","output=","theta=","interrupt-limit="])
opts, args = getopt.getopt(sys.argv[1:], "bc:f:hi:jl:no:O:pt:v", [ "verbose","rna3dmotifs","3dmotifatlas","jar3d","bayespairing","patternmatch","func=",
"help","version","seq=","modules-path=", "first-objective=","output=","theta=",
"interrupt-limit=", "outputf="])
except getopt.GetoptError as err:
print(err)
sys.exit(2)
......@@ -152,7 +155,9 @@ class BiorseoInstance:
self.modules = "desc"
self.func = 'B'
self.inputfile = ""
self.outputf = biorseoDir + "/results/" # default results location
self.finalname = ""
self.outputf = ""
self.output = ""
self.jobcount = 0
self.joblist = []
self.mode = 0 # default is single sequence mode
......@@ -173,7 +178,8 @@ class BiorseoInstance:
print("-p [ --patternmatch ]\t\tUse regular expressions to place modules in the sequence")
print("-j [ --jar3d ]\t\t\tUse JAR3D to place modules in the sequence (requires --3dmotifatlas)")
print("-b [ --bayespairing ]\t\tUse BayesPairing to place modules in the sequence")
print("-o [ --output=… ]\t\tFolder where to output files")
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."
......@@ -195,12 +201,16 @@ class BiorseoInstance:
sys.exit()
elif opt == "-i" or opt == "--seq":
self.inputfile = arg
elif opt == "-o" or opt == "--output":
self.outputf = arg # output file or folder...
elif opt == "-O" or opt == "--outputf":
self.outputf = arg # output folder
if self.outputf[1] != '/':
self.outputf = getcwd() + '/' + self.outputf
if self.outputf[-1] != '/':
self.outputf = self.outputf + '/'
elif opt == "-o" or opt == "--output":
self.output = arg # output file
if self.output[1] != '/':
self.output = getcwd() + '/' + self.output
elif opt == "-f" or opt == "--func":
if arg in ['A', 'B', 'C', 'D']:
self.func = arg
......@@ -237,14 +247,48 @@ class BiorseoInstance:
self.forward_options.append("-c")
self.forward_options.append(arg)
print("saving files to", self.outputf)
if self.outputf != "":
print("saving files to", self.outputf)
# create jobs
self.list_jobs()
# run them
self.execute_jobs()
# subprocess.call(["rm", "-rf", tempDir]) # empty the temp folder
# locate the results at the right place
if self.output != "" and self.outputf != "":
for src_dir, dirs, files in walk(tempDir):
dst_dir = src_dir.replace(tempDir, 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.call(["mv", self.outputf+self.finalname.split('/')[-1], self.output])
elif self.output != "":
subprocess.call(["mv", self.finalname, self.output])
elif self.outputf != "":
for src_dir, dirs, files in walk(tempDir):
dst_dir = src_dir.replace(tempDir, 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.call(["rm", "-rf", tempDir]) # remove the temp folder
def enumerate_loops(self, s):
def resort(unclosedLoops):
......@@ -539,7 +583,8 @@ class BiorseoInstance:
# Read fasta file, which can contain one or several RNAs
RNAcontainer = []
subprocess.call(["mkdir", "-p", self.outputf]) # Create the output folder
if self.outputf != "":
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")
......@@ -610,7 +655,8 @@ class BiorseoInstance:
command = [executable, "-s", fastafile ]
if method_type:
command += [ method_type, csv ]
command += [ "-o", self.outputf + instance.header + ext + self.func, "--function", self.func ]
self.finalname = tempDir + 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))
......