Added cmd_access for a better CLI #118

pyproject.toml

@@ -61,11 +61,8 @@ dependencies = [
 homepage = 'https://github.com/draeger-lab/refinegems'
 documentation = 'https://refinegems.readthedocs.io/en/latest/'
 
-# [project.scripts]
-# data = 'refinegems.databases:main'
-# curate = 'refinegems.curate:main'
-# investigate = 'refinegems.investigate:main'
-# refine = 'refinegems.refine:main'
+[project.scripts]
+refinegems = "refinegems.cmd_access:cli"
 
 # [tool.setuptools.dynamic]
 # version = {attr = "refinegems.VERSION"}

src/refinegems/__init__.py

@@ -1,8 +1,8 @@
-__all__ = ['analysis','classes','curation','utility', 'sboann']
+__all__ = ['analysis','classes','curation','utility', 'sboann', 'cmd_access']
 
 from . import analysis
 from . import classes
 from . import curation
 from . import utility
-
-from . import sboann
+from . import sboann
+from . import cmd_access

src/refinegems/cmd_access.py

@@ -0,0 +1,174 @@
+"""Entry points to the code from the command line.
+"""
+
+__author__ = 'Tobias Fehrenbach, Carolin Brune, Gwendolyn O. Döbel and Famke Bäuerle'
+
+################################################################################
+# Requirements
+################################################################################
+
+from traitlets import default
+import refinegems as rg
+import click
+
+################################################################################
+# Entry points
+################################################################################
+
+@click.group()
+@click.help_option("--help", "-h")
+@click.version_option()
+def cli():
+   """refineGEMs - A toolbox for faster curation and analysis of constraint-based metabolic models
+   
+   This tool provides scripts and functions to curate and analyse a strain-specific GEM with information from multiple 
+   databases. In addition, it offers functions for analysis of multiple GEMs at the same time as well as comparison 
+   reports.
+   """
+
+# ------
+# Set-up
+# ------
+@cli.group()
+def setup():
+   """Set-up tools, folder structure and more for running the program.
+   """
+
+# Get a config file
+# -----------------
+@setup.command()
+@click.option('--filename', '-f', default='config.yaml', type=str, 
+              show_default=True, help='Name (path) to save the config file under.')
+@click.option('--type', '-t', default='basic', type=click.Choice(['media', 'refinegems']), 
+              help='Type of config file to download. Either a file for media configuration or a file to run a refinement pipeline.')
+def config(filename,type):
+    """Download a configuration file (.yaml).
+
+    Download a configuration file to edit for running the complete
+    workflow or provide the media configuration.
+    """
+    rg.utility.set_up.download_config(filename, type)
+
+# @TODO: Download a file with all media for a specific database?
+# Handle medium / media database
+# ------------------------------
+@setup.command()
+@click.option('--list', is_flag=True, default=False, help='List the names of the media in the database.')
+#@click.option('--copy', is_flag=False, flag_value='./media.csv', default=None, type=click.Path(exists=False), 
+# help='Produce and save a copy of the media database.')
+def medium(list): #,copy
+    """Access the in-build media database.
+
+    Can be used to either check the available media or to make a copy for further use.
+    """
+    if list:
+        possible_media = rg.utility.io.load_a_table_from_database('medium', False)['name'].to_list()
+        media = '|'.join(possible_media)
+        print(media)
+'''
+    if copy:
+        db = specimen.classes.medium.load_media_db()
+        specimen.classes.medium.save_db(db,click.format_filename(copy))
+'''
+
+
+# --------------
+# Polish a model
+# --------------
+@cli.group()
+def polish():
+	"""Polish a model created by an automatic reconstruction pipeline. CLeans up the notes fields, changes qualifiers and 
+ 	annotations to be MIRIAM-compliant and fixes the initial biomass equation to add up to 1mmol/gDW/h.
+	"""
+
+# Polish an automatically generated reconstruction
+# ------------------------------------------------
+@polish.command()
+@click.argument('model', type=str)
+@click.argument('email', type=str)
+@click.argument('path', type=str)
+@click.option('-i','--id_db', default='BiGG', type=str, help='Main database where identifiers in model come from')
+@click.option('-r', '--refseq_gff', default=None, type=str, help='Path to RefSeq GFF file of organism')
+@click.option('-p', '--protein_fasta', default=None, type=str, help='File used as input for CarveMe')
+@click.option('-l', '--lab_strain', default=False, type=bool, help='True if the strain was sequenced in a local lab')
+@click.option('-k', '--kegg_organism_id', default=None, type=str, help='KEGG organism identifier')
+def polish(model,email,path,id_db,refseq_gff,protein_fasta,lab_strain,kegg_organism_id):
+   """Completes all steps to polish a model
+   
+   (Tested for models having either BiGG or VMH identifiers.)
+   """
+   rg.curation.polish.polish(model, email, id_db, refseq_gff, protein_fasta, lab_strain, kegg_organism_id, path)
+
+
+# ----------------------------------------------------------------------------------
+# Find and fill gaps in a model automatically/Fill gaps with manually created tables
+# ----------------------------------------------------------------------------------
+@cli.group()
+def gaps():
+	"""If requested finds gaps in a model based on the gene products in the model and either files from biocyc or via the
+ 	KEGG API.
+	If requested fills gaps either via the automatically obtained missing entities or via a manually created file 
+ 	provided by the user.
+	"""
+
+# Find gaps via genes
+# -------------------
+@gapfill.command()
+@click.argument('model', type=str)
+def find(model,gff_file,organismid,gapfill_params,filename):
+	"""Find gaps in a model based on the genes/gene products of the underlying organism
+	"""
+	rg.curation.gapfill.gap_analysis(model, gff_file, organismid, gapfill_params, filename)
+
+# Fill gaps via file
+# ------------------
+@gapfill.command()
+@click.argument('model', type=str)
+def fill(model,gap_analysis_result):
+	"""Fill gaps in a model based on a user-provided input file
+	"""
+	rg.curation.gapfill.gapfill_model(model, gap_analysis_result)
+
+# Find and fill gaps via genes
+# ----------------------------
+@gapfill.command()
+@click.argument('model', type=str)
+def complete(model,gapfill_params,filename):
+	"""Find and fill gaps based on the genes/gene products automatically
+	"""
+	rg.curation.gapfill.gapfill(model, gapfill_params, filename)
+
+
+# --------------
+# Refine a model
+# --------------
+@cli.group()
+def refine():
+   """Refine a model. Includes steps like biomass, charges, SBO annotation, reaction direction correction and addition 
+   of Pathways and further gene product annotations.
+   """
+
+# Annotation-related clean-up & Additional annotations
+# ---------------------------
+@refine.group()
+def annot():
+	"""Clean-up annotations by adding MIRIAM-compliant qualifiers, changing URIs into the correct form, adding more 
+ 	specific SBO annotations and synchronising all annotations to BioCyc. Additionally, adds gene product annotations 
+  	either from the GFF file of the organism or via KEGG.
+	"""
+
+
+# -----------------------------------------------
+# Analyse a model/multiple models including a comparison
+# -----------------------------------------------
+@cli.group()
+def analyse():
+	"""Analyse a model by testing for auxotrophies and growth on different media along with finding EGCs and looking at 
+ 	overall model statistics. 
+	"""
+
+
+# data = 'refinegems.databases:main'
+# curate = 'refinegems.curate:main'
+# analysis = 'refinegems.analysis:main'
+# refine = 'refinegems.refine:main'