MultiMM 1.0.22__tar.gz → 1.0.24__tar.gz

{multimm-1.0.22 → multimm-1.0.24}/MultiMM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MultiMM
-Version: 1.0.22
+Version: 1.0.24
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Home-page: https://github.com/SFGLab/MultiMM
 Author: Sebastian Korsak
@@ -237,8 +237,9 @@ Therefore, it is advisable to read the paper and understand well the meaning of
 | Argument Name                | Type         | Value       | Units         | Description |
 |------------------------------|--------------|-------------|---------------|-------------|
 | PLATFORM                     | str          | CPU        | CPU          | name of the platform. Available choices: CPU, OpenCL, CUDA. |
+| CPU_THREADS                  | int          | None        | None          | Number of CPU threads (in case that CPU is chosen as platform). |
 | DEVICE                       | str          | None        | None          | device index for CUDA or OpenCL (count from 0) |
-| MAGIC_ARGUMENT               | str          | None        | None          | Helping function to specify parameters of simulation. Choose 'GENE', 'CHROM' or 'GW' depending on the resolution of interest. |
+| MODELLING_LEVEL               | str          | None        | None          | Helping function to specify parameters of simulation. Choose 'GENE', 'CHROM' or 'GW' depending on the resolution of interest. |
 | INITIAL_STRUCTURE_PATH       | str          | None        | None          | Path to CIF file. |
 | BUILD_INITIAL_STRUCTURE      | bool         | True        | None          | To build a new initial structure. |
 | INITIAL_STRUCTURE_TYPE       | str          | hilbert     | None          | you can choose between: hilbert, circle, rw, confined_rw, self_avoiding_rw, helix, spiral, sphere, knot. |
@@ -255,7 +256,7 @@ Therefore, it is advisable to read the paper and understand well the meaning of
 | GENE_TSV      | str  | ''    | None   | A .tsv with genes and their locations in the genome. |
 | GENE_NAME     | str  | ''    | None   | The name of the gene of interest. |
 | GENE_ID       | str  | ''    | None   | The id of the gene of interest. |
-| GENE_WINDOW   | int  | 200000| bp     | The window around the area of the gene of interest. |
+| GENE_WINDOW   | int  | 500000| bp     | The window around the area of the gene of interest. |
 | LOC_START                    | int          | None        | None          | Starting region coordinate (*in case that you do not want to model the whole genome*). |
 | LOC_END                      | int          | None        | None          | Ending region coordinate (*in case that you do not want to model the whole genome*). |
 | CHROM                        | str          | None        | None          | Chromosome that corresponds the the modelling region of interest (*in case that you do not want to model the whole genome*). |

{multimm-1.0.22 → multimm-1.0.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MultiMM
-Version: 1.0.22
+Version: 1.0.24
 Summary: A tool for chromatin modeling from nucleosomes to chromosomal territories.
 Home-page: https://github.com/SFGLab/MultiMM
 Author: Sebastian Korsak
@@ -237,8 +237,9 @@ Therefore, it is advisable to read the paper and understand well the meaning of
 | Argument Name                | Type         | Value       | Units         | Description |
 |------------------------------|--------------|-------------|---------------|-------------|
 | PLATFORM                     | str          | CPU        | CPU          | name of the platform. Available choices: CPU, OpenCL, CUDA. |
+| CPU_THREADS                  | int          | None        | None          | Number of CPU threads (in case that CPU is chosen as platform). |
 | DEVICE                       | str          | None        | None          | device index for CUDA or OpenCL (count from 0) |
-| MAGIC_ARGUMENT               | str          | None        | None          | Helping function to specify parameters of simulation. Choose 'GENE', 'CHROM' or 'GW' depending on the resolution of interest. |
+| MODELLING_LEVEL               | str          | None        | None          | Helping function to specify parameters of simulation. Choose 'GENE', 'CHROM' or 'GW' depending on the resolution of interest. |
 | INITIAL_STRUCTURE_PATH       | str          | None        | None          | Path to CIF file. |
 | BUILD_INITIAL_STRUCTURE      | bool         | True        | None          | To build a new initial structure. |
 | INITIAL_STRUCTURE_TYPE       | str          | hilbert     | None          | you can choose between: hilbert, circle, rw, confined_rw, self_avoiding_rw, helix, spiral, sphere, knot. |
@@ -255,7 +256,7 @@ Therefore, it is advisable to read the paper and understand well the meaning of
 | GENE_TSV      | str  | ''    | None   | A .tsv with genes and their locations in the genome. |
 | GENE_NAME     | str  | ''    | None   | The name of the gene of interest. |
 | GENE_ID       | str  | ''    | None   | The id of the gene of interest. |
-| GENE_WINDOW   | int  | 200000| bp     | The window around the area of the gene of interest. |
+| GENE_WINDOW   | int  | 500000| bp     | The window around the area of the gene of interest. |
 | LOC_START                    | int          | None        | None          | Starting region coordinate (*in case that you do not want to model the whole genome*). |
 | LOC_END                      | int          | None        | None          | Ending region coordinate (*in case that you do not want to model the whole genome*). |
 | CHROM                        | str          | None        | None          | Chromosome that corresponds the the modelling region of interest (*in case that you do not want to model the whole genome*). |

{multimm-1.0.22 → multimm-1.0.24}/README.md

@@ -196,8 +196,9 @@ Therefore, it is advisable to read the paper and understand well the meaning of
 | Argument Name                | Type         | Value       | Units         | Description |
 |------------------------------|--------------|-------------|---------------|-------------|
 | PLATFORM                     | str          | CPU        | CPU          | name of the platform. Available choices: CPU, OpenCL, CUDA. |
+| CPU_THREADS                  | int          | None        | None          | Number of CPU threads (in case that CPU is chosen as platform). |
 | DEVICE                       | str          | None        | None          | device index for CUDA or OpenCL (count from 0) |
-| MAGIC_ARGUMENT               | str          | None        | None          | Helping function to specify parameters of simulation. Choose 'GENE', 'CHROM' or 'GW' depending on the resolution of interest. |
+| MODELLING_LEVEL               | str          | None        | None          | Helping function to specify parameters of simulation. Choose 'GENE', 'CHROM' or 'GW' depending on the resolution of interest. |
 | INITIAL_STRUCTURE_PATH       | str          | None        | None          | Path to CIF file. |
 | BUILD_INITIAL_STRUCTURE      | bool         | True        | None          | To build a new initial structure. |
 | INITIAL_STRUCTURE_TYPE       | str          | hilbert     | None          | you can choose between: hilbert, circle, rw, confined_rw, self_avoiding_rw, helix, spiral, sphere, knot. |
@@ -214,7 +215,7 @@ Therefore, it is advisable to read the paper and understand well the meaning of
 | GENE_TSV      | str  | ''    | None   | A .tsv with genes and their locations in the genome. |
 | GENE_NAME     | str  | ''    | None   | The name of the gene of interest. |
 | GENE_ID       | str  | ''    | None   | The id of the gene of interest. |
-| GENE_WINDOW   | int  | 200000| bp     | The window around the area of the gene of interest. |
+| GENE_WINDOW   | int  | 500000| bp     | The window around the area of the gene of interest. |
 | LOC_START                    | int          | None        | None          | Starting region coordinate (*in case that you do not want to model the whole genome*). |
 | LOC_END                      | int          | None        | None          | Ending region coordinate (*in case that you do not want to model the whole genome*). |
 | CHROM                        | str          | None        | None          | Chromosome that corresponds the the modelling region of interest (*in case that you do not want to model the whole genome*). |

{multimm-1.0.22 → multimm-1.0.24}/setup.py

@@ -6,7 +6,7 @@ with open('README.md', 'r', encoding='utf-8') as f:
 
 setup(
     name='MultiMM',  # Package name
-    version='1.0.22',  # Version of the software
+    version='1.0.24',  # Version of the software
     description='A tool for chromatin modeling from nucleosomes to chromosomal territories.',
     long_description=long_description,
     long_description_content_type='text/markdown',

{multimm-1.0.22 → multimm-1.0.24}/simulation/__init__.py

@@ -1,4 +1,4 @@
 # Importing specific functions or classes from submodules
 from .run import main
 
-__version__ = "1.0.22"
+__version__ = "1.0.24"

{multimm-1.0.22 → multimm-1.0.24}/simulation/args_definition.py

@@ -133,8 +133,9 @@ available_platforms = [mm.Platform.getPlatform(i).getName() for i in range(mm.Pl
 args = ListOfArgs([
     # Platform settings
     Arg('PLATFORM', help=f"name of the platform. Available choices: {' '.join(available_platforms)}", type=str, default='CPU', val='CPU'),
+    Arg('CPU_THREADS', help=f"The number of CPU threads (in case you would like to specify them).", type=int, default='', val=''),
     Arg('DEVICE', help="device index for CUDA or OpenCL (count from 0)", type=str, default='', val=''),
-    Arg('MAGIC_ARGUMENT', help="Choose 'GENE' or 'REGION' for gene or TAD level, 'CHROM' for chromosome leve, and 'GW' for genome level. It will setup some parameters for you and print you helpful comments.", type=str, default='', val=''),
+    Arg('MODELLING_LEVEL', help="Choose 'GENE' or 'REGION' for gene or TAD level, 'CHROM' for chromosome leve, and 'GW' for genome level. It will setup some parameters for you and print you helpful comments.", type=str, default='', val=''),
     
     # Input data
     Arg('INITIAL_STRUCTURE_PATH', help="Path to CIF file.", type=str, default='', val=''),
@@ -151,7 +152,7 @@ args = ListOfArgs([
     Arg('GENE_TSV', help="A .tsv with genes and their locations in the genome.", type=str, default='', val=''),
     Arg('GENE_NAME', help="The name of the gene of interest.", type=str, default='', val=''),
     Arg('GENE_ID', help="The id of the gene of interest.", type=str, default='', val=''),
-    Arg('GENE_WINDOW', help="The window around of the area around the gene of interest.", type=int, default='200000', val='200000'),
+    Arg('GENE_WINDOW', help="The window around of the area around the gene of interest.", type=int, default='500000', val='500000'),
     Arg('ATACSEQ_PATH', help="A .bw or .BigWig file path with atacseq data. It is not required.", type=str, default='', val=''),
     Arg('OUT_PATH', help="Output folder name.", type=str, default='results', val='results'),
     Arg('LOC_START', help="Starting region coordinate.", type=int, default='', val=''),

{multimm-1.0.22 → multimm-1.0.24}/simulation/model.py

@@ -101,7 +101,7 @@ class MultiMM:
     def convenient_argument_changer(self):
         self.args.NUC_DO_INTERPOLATION = False
         self.args.ATACSEQ_PATH = None
-        if self.args.MAGIC_ARGUMENT=='GENE' or self.args.MAGIC_ARGUMENT=='REGION' or self.args.MAGIC_ARGUMENT=='TAD':
+        if self.args.MODELLING_LEVEL=='GENE' or self.args.MODELLING_LEVEL=='REGION' or self.args.MODELLING_LEVEL=='TAD':
             print('\033[91m' + 'MAGIC COMMENT: For gene level it is needed to provide a loops_path, a gene_tsv file, and a gene_name or gene_id to specify the target gene of interest.'+ '\033[0m')
             self.args.N_BEADS=1000
             self.args.SC_USE_SPHERICAL_CONTAINER=False
@@ -113,7 +113,7 @@ class MultiMM:
             self.args.SHUFFLE_CHROMS=False
             self.args.SIM_RUN_MD=True
             self.args.SIM_N_STEPS=10000
-        elif self.args.MAGIC_ARGUMENT=='CHROMOSOME' or self.args.MAGIC_ARGUMENT=='CHROM' or self.args.MAGIC_ARGUMENT=='COMP':
+        elif self.args.MODELLING_LEVEL=='CHROMOSOME' or self.args.MODELLING_LEVEL=='CHROM' or self.args.MODELLING_LEVEL=='COMP':
             print('\033[91m' + 'MAGIC COMMENT: For chromosome level it is needed to provide a loops_path. Do not forget to specify the beggining and end of your chromosome. You can remove the centromers or telomers that are in the boundaries. You can optionally add an eigenvector_tsv to include block-copolymer forces.'+ '\033[0m')
             self.args.N_BEADS=20000
             self.args.SC_USE_SPHERICAL_CONTAINER=False
@@ -124,7 +124,7 @@ class MultiMM:
             self.args.CF_USE_CENTRAL_FORCE=False
             self.args.SIM_RUN_MD=True
             self.args.SIM_N_STEPS=10000
-        elif self.args.MAGIC_ARGUMENT=='GW' or self.args.MAGIC_ARGUMENT=='GENOME':
+        elif self.args.MODELLING_LEVEL=='GW' or self.args.MODELLING_LEVEL=='GENOME':
             print('\033[91m' + 'MAGIC COMMENT: For gw level it is needed to provide a loops_path. You can optionally add an eigenvector_tsv to include block-copolymer forces.'+ '\033[0m')
             self.args.N_BEADS=200000
             self.args.SC_USE_SPHERICAL_CONTAINER=True
@@ -309,6 +309,8 @@ class MultiMM:
         except Exception as e:
             print(f"Failed to find {self.args.PLATFORM}: {e}. Falling back to CPU.")
             platform = mm.Platform.getPlatformByName('CPU')
+        if self.args.PLATFORM=='CPU' and self.args.CPU_THREADS!=None:
+            platform.setPropertyDefaultValue('Threads', f'{self.args.CPU_THREADS}')
         
         # Run the simulation
         self.simulation = Simulation(self.pdb.topology, self.system, self.integrator, platform)     

{multimm-1.0.22 → multimm-1.0.24}/simulation/utils.py

@@ -289,6 +289,8 @@ def import_mns_from_bedpe(bedpe_file, N_beads, coords=None, chrom=None, threshol
     mns, cs = np.vstack((loops['ms'].values[counts>threshold], loops['ns'].values[counts>threshold])), counts[counts>threshold]
     mns, idxs = np.unique(mns,axis=1,return_index=True)
     cs = cs[idxs]
+    if cs.size == 0:
+        raise ValueError("The region of interest does not include loops. Please try with longer modelling region or increase the window around the gene.")
     ms, ns = mns[0,:], mns[1,:]
     ms[ms>=N_beads],ns[ns>=N_beads]=N_beads-1, N_beads-1
     ms,ns,cs = ms[ns>ms+min_loop_dist], ns[ns>ms+min_loop_dist], cs[ns>ms+min_loop_dist]