cmpb update + user input #8

docs/source/conf.py

@@ -19,6 +19,7 @@
 #
 import os
 import sys
+from pathlib import Path
 sys.path.insert(0, os.path.abspath('../../src/'))
 
 # -- General configuration ---------------------------------------------------
@@ -56,14 +57,14 @@
 html_css_files = ['custom_theme.css']
 
 # Adds logo to documentation page
-html_logo = 'images/LogoSPECIMEN.png'
+html_logo = str(Path('images','LogoSPECIMEN.png'))
 html_theme_options = {
     'logo_only': True,
     'display_version': False
 }
 
 #Adds logo as favicon to tab
-html_favicon = 'images/LogoSPECIMEN.png'
+html_favicon = str(Path('images','LogoSPECIMEN.png'))
 
 # Changes code highlighting
 pygments_style = 'blinds-light'

pyproject.toml

@@ -41,7 +41,7 @@ dependencies = [
     'seaborn',
     'tqdm',
     'z3-solver',
-    'multiprocess~>=0.70.16'
+    'multiprocess>=0.70.16'
 ]
 # additional missing tools:
 #    EntrezDirect

src/specimen/cmpb/workflow.py

@@ -10,11 +10,12 @@
 import pandas as pd
 from datetime import date
 from pathlib import Path
+from typing import Union
 
 import warnings
 import yaml
 
-from cobra import Reaction
+from cobra import Reaction,Model
 from libsbml import readSBML
 
 from refinegems.analysis import growth
@@ -48,9 +49,28 @@
 #   in the run function: current_model means the cobrapy model, 
 #   while current_libmodel means the libsbml model
 
-def run(configpath:str):
-
-    def between_growth_test(model, cfg, step):
+def run(configpath:Union[str,None]=None):
+    """Run the CarveMe
+
+    Args:
+        - configpath (Union[str,None]): 
+            The Path to a configuration file. If none given, prompts the user to enter the needed 
+            information step by step.
+            Defaults to None.
+    """
+
+    def between_growth_test(model: Model, cfg:dict, step:str):
+        """Helper function for :py:func:`~specimen.cmpb.workflow.run`. 
+        Run a growth test on a model with the options set in the config file.
+
+        Args:
+            - model (Model): 
+                The cobra.Model for testing the growth.
+            - cfg (dict): 
+                The loaded configuration file.
+            - step (str): 
+                Descriptive string for the current step of the pipeline (important for saving the output).
+        """
         # try to set objective to growth
         growth_func_list = test_biomass_presence(model)
         if growth_func_list:
@@ -66,7 +86,18 @@ def between_growth_test(model, cfg, step):
             mes = f'No growth/biomass function detected, growth simulation for step {step} will be skipped.'
             warnings.warn(mes)
 
-    def between_analysis(model, cfg, step):
+    def between_analysis(model: Model, cfg:dict, step:str):
+        """Helper function for :py:func:`~specimen.cmpb.workflow.run`. 
+        Run a memote and/or stats test on a model with the options set in the config file.
+
+        Args:
+            - model (Model): 
+                The cobra.Model for testing.
+            - cfg (dict): 
+                The loaded configuration file.
+            - step (str): 
+                Descriptive string for the current step of the pipeline (important for saving the output).
+        """
         # optional analysis
         if cfg['general']['memote_always_on']:
             run_memote(model, 'html', 

src/specimen/util/set_up.py

@@ -16,7 +16,7 @@
 from importlib.resources import files
 from pathlib import Path
 from tqdm import tqdm
-from typing import Literal
+from typing import Literal,Union
 
 from refinegems.utility.set_up import download_config as rg_config
 from refinegems.utility.io import load_a_table_from_database
@@ -302,7 +302,7 @@ def dict_recursive_check(dictA:dict, key:str=None):
 
 # @TODO
 #    is it still correct after all the changes???
-def save_cmpb_user_input(configpath: str) -> dict[str: str]:
+def old_save_cmpb_user_input(configpath: str) -> dict[str: str]:
     """This aims to collect user input from the command line to create a cmpb config file, 
     will also save the user input to a config if no config was given
 
@@ -482,3 +482,132 @@ def save_cmpb_user_input(configpath: str) -> dict[str: str]:
         print('Your input was saved as yaml to '+ user_input['out_path'] + 'user_input_' + str(today) + '.yaml')
         return user_input
 
+
+def save_cmpb_user_input(configpath: Union[str,None]=None) -> dict[str: str]:
+
+        print('No config or no valid config given, you will be asked for input')
+        user_input = {}
+
+        config_file = files('specimen.data.config').joinpath('cmpb_config.yaml')
+        with open(config_file, "r") as cfg:
+            config = yaml.load(cfg, Loader=yaml.loader.FullLoader)
+
+        # if model, get path
+        has_model = click.prompt('Do you already have a draft model e.g. created with CarveMe? (y/n)')
+        while(True):
+            match has_model:
+                case 'y':
+                    modelpath = click.prompt('Enter the path to your model')
+                    config['input']['modelpath'] = modelpath
+                    break
+                case 'n':
+                    break
+                case _:
+                    has_model = click.prompt('')
+
+        # required input
+        # --------------
+        print('------------')
+        print('The following information is REQUIRED for the pipeline')
+        print('------------')
+        config['input']['annotated_genome'] = click.prompt('Enter the path to your annotated genome file')
+        config['input']['mediapath'] = click.prompt('Enter the path to a media configuration file for growth simulation')
+
+        # general options
+        # ---------------
+        print('------------')
+        print('General options')
+        print('------------')
+
+        # output directory
+        config['general']['dir'] = click.prompt('Enter your desired output directory path')
+
+        # colour 
+        set_col = click.prompt('Do you want to use the default colour map YlGn for the visualisation? (y/n)')
+        while(True):
+            match set_col:
+                case 'n':
+                    colours = click.prompt('Enter your choosen colour scheme')
+                    config['general']['colours'] = colours
+                    break
+                case 'y':
+                    break
+                case _:
+                    set_col = click.prompt('')
+
+        # save all models or not
+        save_models = click.prompt('Do you want to save the model separatly after each step? (y/n)')
+        while(True):
+            match save_models:
+                case 'y':
+                    config['general']['save_all_models'] = True
+                    break
+                case 'n':
+                    config['general']['save_all_models'] = False
+                    break
+                case _:
+                    save_models = click.prompt('')
+
+        # run memote always y/n
+        run_memote = click.prompt('Do you want run memote after each step? (y/n)')
+        while(True):
+            match run_memote:
+                case 'y':
+                    config['general']['memote_always_on'] = True
+                    break
+                case 'n':
+                    config['general']['memote_always_on'] = False
+                    break
+                case _:
+                    run_memote = click.prompt('')
+
+        # run stats always y/n
+        models_stats = click.prompt('Do you want run memote after each step? (y/n)')
+        while(True):
+            match models_stats:
+                case 'y':
+                    config['general']['stats_always_on'] = True
+                    break
+                case 'n':
+                    config['general']['stats_always_on'] = False
+                    break
+                case _:
+                    models_stats = click.prompt('')
+
+        # some additional, sometimes required, sometimes optional files
+        refseq = click.prompt('If you want to run a gap analysis with KEGG or have a CarveMe model, please enter the path to your refseq gff file')
+        config['general']['refseq_organism_id'] = refseq
+
+        kegg_org_id = click.prompt('If you want to run a gap analysis with KEGG or have a CarveMe model, please enter the path to your refseq gff file')
+        config['general']['refseq_organism_id'] = kegg_org_id
+
+        # part-specific 
+        # -------------
+        print('------------')
+        print('Part-specific options')
+        print('------------')
+
+        # model polish
+
+        # gapfilling
+        # RECYCLE OLD FUNCTION
+
+        # kegg pathways as groups
+        kegg_pw_groups = click.prompt('Do you want to add KEGG pathways as groups to the model? (y/n)')
+        config['kegg_pathway_groups'] = kegg_pw_groups
+
+        # resolve duplicates
+
+        # BOF
+
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