Change magic argument to modelling level

Author: BlackPianoCat

README.md

@@ -198,7 +198,7 @@ Therefore, it is advisable to read the paper and understand well the meaning of
 | 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. |

simulation/args_definition.py

@@ -135,7 +135,7 @@ def write_config_file(self):
     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=''),

simulation/model.py

@@ -101,7 +101,7 @@ def __init__(self,args):
     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 @@ def convenient_argument_changer(self):
             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 @@ def convenient_argument_changer(self):
             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