Renamed the tool

.gitignore

@@ -10,8 +10,8 @@ hg19-tss-centered-10kb-10species.mc9nr.feather
 test_dump
 code
 deps
-cmi/dependencies
-CMI.egg-info
+crgem/dependencies
+CRGEM.egg-info
 build/
 _build/
 __pycache__

README.md

@@ -2,10 +2,10 @@
 ![workflow badge](https://github.com/thoughtworks/cell-reprogram-workflow/actions/workflows/setup-test-workflow.yml/badge.svg)
 
 
-### CMI: Cellular conversion using Mechanistic driven Integrated workflow
+### CRGEM: Cellular Reprogramming using mechanism-driven Gene Expression Modulation
 
 A framework created using already available tools and databases, to perform cellular reprogramming computationally. 
-To carry out tool specific task using the various tools available separately, the researchers need to go through the tools individually. CMI ease their work by integrating the tools at one place.
+To carry out tool specific task using the various tools available separately, the researchers need to go through the tools individually. CRGEM ease their work by integrating the tools at one place.
 With this integration of the functionalities researchers can invest time in biological inferences and experimentally verifying the key modulators and their effects.
 
 <hr>
@@ -91,43 +91,43 @@ The starting cell population and terminal cell population cluster IDs to be ener
 ### Commands
 - <u>stage</u>: all (TransSynW + PAGA + SIGNET + TRRUST + Cytoscape + Uniprot)  
 
-    cmi run all --artefacts ./artefacts/[directory_name] --params [start_cell population] [start and terminal_cell population] [annotation file] [terminal cell cluster ID] [startaing cell cluster ID] ./data/terminal.csv ./data/trrust_rawdata_human.tsv  
+    crgem run all --artefacts ./artefacts/[directory_name] --params [start_cell population] [start and terminal_cell population] [annotation file] [terminal cell cluster ID] [startaing cell cluster ID] ./data/terminal.csv ./data/trrust_rawdata_human.tsv  
 
-    Eg: cmi run all --artefacts ./artefacts/temp --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES ./data/terminal.csv ./data/trrust_rawdata_human.tsv
+    Eg: crgem run all --artefacts ./artefacts/temp --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES ./data/terminal.csv ./data/trrust_rawdata_human.tsv
 
 - <u>stage</u>: generate_hypothesis (TransSynW)  
 
-    cmi run generate_hypothesis --artefacts ./artefacts/[directory_name] --params [start_cell population] [start and terminal_cell population] [annotation file] [terminal cell cluster ID]
+    crgem run generate_hypothesis --artefacts ./artefacts/[directory_name] --params [start_cell population] [start and terminal_cell population] [annotation file] [terminal cell cluster ID]
 
-    Eg: cmi run generate_hypothesis --artefacts ./artefacts/[directory_name] --params start.txt start_terminal.txt annotation.txt HPROGFPM
+    Eg: crgem run generate_hypothesis --artefacts ./artefacts/[directory_name] --params start.txt start_terminal.txt annotation.txt HPROGFPM
 
 - <u>stage</u>: mechanistic insights (TransSynW + PAGA)  
 
-    cmi run mechanistic insights --artefacts ./artefacts/[directory_name] --params [start_cell population] [start and terminal_cell population] [annotation file] [terminal cell cluster ID] [startaing cell cluster ID]
+    crgem run mechanistic insights --artefacts ./artefacts/[directory_name] --params [start_cell population] [start and terminal_cell population] [annotation file] [terminal cell cluster ID] [startaing cell cluster ID]
 
-    Eg: cmi run mechanistic_insights --artefacts ./artefacts/temp --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES
+    Eg: crgem run mechanistic_insights --artefacts ./artefacts/temp --params start.txt start_terminal.txt annotation.txt HPROGFPM HNES
 
 - <u>stage</u>: grn inference (SIGNET)  
 
-    cmi run grn_inference --artefacts ./artefacts/[directory_name] --params ./data/terminal.csv  
+    crgem run grn_inference --artefacts ./artefacts/[directory_name] --params ./data/terminal.csv  
 
-    Eg: cmi run grn_inference --artefacts ./artefacts/temp --params ./data/terminal.csv
+    Eg: crgem run grn_inference --artefacts ./artefacts/temp --params ./data/terminal.csv
 
 - <u>stage</u>: trrust analysis (TRRUST)  
 
-    cmi run trrust_analysis --artefacts ./artefacts/[directory_name] --params ./data/trrust_rawdata_human.tsv
+    crgem run trrust_analysis --artefacts ./artefacts/[directory_name] --params ./data/trrust_rawdata_human.tsv
 
-    Eg: cmi run trrust_analysis --artefacts ./artefacts/temp --params ./data/trrust_rawdata_human.tsv 
+    Eg: crgem run trrust_analysis --artefacts ./artefacts/temp --params ./data/trrust_rawdata_human.tsv 
 
 
 - <u>stage</u>: gene network (Cytoscape)  
 
-    cmi run create_network --artefacts ./artefacts/[directory_name] --params ./artefacts/[directory_name]/Trrust_Analysis/trrust_analysis.csv
+    crgem run create_network --artefacts ./artefacts/[directory_name] --params ./artefacts/[directory_name]/Trrust_Analysis/trrust_analysis.csv
 
-    Eg: cmi run create_network --artefacts ./artefacts/temp --params ./artefacts/temp/Trrust_Analysis/trrust_analysis.csv 
+    Eg: crgem run create_network --artefacts ./artefacts/temp --params ./artefacts/temp/Trrust_Analysis/trrust_analysis.csv 
 
 - <u>stage</u>: functional analysis (Uniprot)  
 
-    cmi run functional_analysis --artefacts ./artefacts/[directory_name] /Trrust_analysis/transsynw_genes.csv /Trrust_analysis/signet_genes.csv  
+    crgem run functional_analysis --artefacts ./artefacts/[directory_name] /Trrust_analysis/transsynw_genes.csv /Trrust_analysis/signet_genes.csv  
 
-    Eg: cmi run functional_analysis --artefacts ./artefacts/temp /Trrust_analysis/transsynw_genes.csv /Trrust_analysis/signet_genes.csv
+    Eg: crgem run functional_analysis --artefacts ./artefacts/temp /Trrust_analysis/transsynw_genes.csv /Trrust_analysis/signet_genes.csv

cmi/stages/create_network.py → crgem/stages/create_network.py

@@ -6,7 +6,7 @@
 import json
 import requests
 import logging
-from cmi.common import clean_up
+from crgem.common import clean_up
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)

cmi/stages/functional_analysis.py → crgem/stages/functional_analysis.py

@@ -3,8 +3,8 @@
 import os
 import logging
 import pandas as pd
-from cmi.common import clean_up
-from cmi.common import http_post, http_request
+from crgem.common import clean_up
+from crgem.common import http_post, http_request
 
 
 logger = logging.getLogger(__name__)

cmi/stages/generate_hypothesis.py → crgem/stages/generate_hypothesis.py

@@ -1,7 +1,7 @@
 "generate_hypothesis.py"
 
 
-from cmi.tool.transsynw_tool import runTranssynW
+from crgem.tool.transsynw_tool import runTranssynW
 import logging
 
 logger = logging.getLogger(__name__)

cmi/stages/grn_inference.py → crgem/stages/grn_inference.py

@@ -1,6 +1,6 @@
 "grn_inference.py"
 
-from cmi.tool.signet_tool import runSignetpy, runR
+from crgem.tool.signet_tool import runSignetpy, runR
 import logging
 
 logger = logging.getLogger(__name__)

cmi/stages/mechanistic_insights.py → crgem/stages/mechanistic_insights.py

@@ -1,8 +1,8 @@
 "mechanistic_insights.py"
 
 
-from cmi.tool.transsynw_tool import runTranssynW
-from cmi.tool.paga_tool import runPaga
+from crgem.tool.transsynw_tool import runTranssynW
+from crgem.tool.paga_tool import runPaga
 
 import logging
 

cmi/stages/trrust_analysis.py → crgem/stages/trrust_analysis.py

@@ -2,7 +2,7 @@
 import pandas as pd
 import numpy as np
 import os
-from cmi.common import clean_up
+from crgem.common import clean_up
 import logging
 
 

cmi/tool/Signet/SIGNET_GRN_prediction.R → crgem/tool/Signet/SIGNET_GRN_prediction.R

@@ -4,7 +4,7 @@ args= commandArgs(trailingOnly = TRUE)
 in_path = args[1]
 
 library(RcisTarget)
-source('./cmi/tool/Signet/SIGNET.R')
+source('./crgem/tool/Signet/SIGNET.R')
 
 # Select motif database to use (annotations)
 data("motifAnnotations_hgnc")

cmi/tool/paga_tool.py → crgem/tool/paga_tool.py

@@ -1,5 +1,5 @@
 "paga_tool.py"
-from cmi.tool.PAGA import paga
+from crgem.tool.PAGA import paga
 
 def runPaga(*args):
     paga(*args)

cmi/tool/signet_tool.py → crgem/tool/signet_tool.py

@@ -3,7 +3,7 @@
 import subprocess
 import os
 import sys
-from cmi.common import clean_up
+from crgem.common import clean_up
 
 # from dependencies.Signet.SIGNET import signet
 code_path = './Signet'

cmi/tool/transsynw_tool.py → crgem/tool/transsynw_tool.py

@@ -4,7 +4,7 @@
 import subprocess
 import os
 import sys
-from cmi.common import clean_up
+from crgem.common import clean_up
 cwd = os.getcwd()
 print("cwd:", cwd)
 abs_path = os.path.dirname(__file__)

setup.py

@@ -2,7 +2,7 @@
 from setuptools import setup, find_packages
 
 setup_info = dict(
-    name='CMI',
+    name='CRGEM',
     version='0.1',
     author='E4R',
     author_email='[email protected]',
@@ -18,16 +18,16 @@
     long_description_content_type='text/markdown',
     license='MIT',
     # Package info
-    packages=['cmi'] + ['cmi.' + pkg for pkg in find_packages('cmi')],
+    packages=['crgem'] + ['crgem.' + pkg for pkg in find_packages('crgem')],
     package_data={
-        "cmi.tool.Signet": ["*.R", "*.txt"],
-        "cmi.dependencies": ["transsynw/*/*", "SIGNET.py"]
+        "crgem.tool.Signet": ["*.R", "*.txt"],
+        "crgem.dependencies": ["transsynw/*/*", "SIGNET.py"]
 
     },
     # Add _ prefix to the names of temporary build dirs
     options={'build': {'build_base': '_build'}, },
     zip_safe=True,
-    scripts=['bin/cmi'],
+    scripts=['bin/crgem'],
     install_requires=[
     'anndata==0.10.3',
     'array-api-compat==1.4',

setup.sh

@@ -1,8 +1,8 @@
 
 # TransSynW dependencies
 
-mkdir ./cmi/dependencies
-cd ./cmi/dependencies
+mkdir ./crgem/dependencies
+cd ./crgem/dependencies
 touch __init__.py
 git clone --depth=1 https://gitlab.lcsb.uni.lu/CBG/transsynw.git transsynw
 

test_setup.sh

@@ -8,8 +8,8 @@ python -m pip install --upgrade pip
 pip install pytest
 pip install -r requirements.txt
 
-mkdir ./cmi/dependencies
-cd ./cmi/dependencies
+mkdir ./crgem/dependencies
+cd ./crgem/dependencies
 touch __init__.py
 git clone --depth=1 https://gitlab.lcsb.uni.lu/CBG/transsynw.git transsynw
 

tests/e2e/test_create_network.py

@@ -4,7 +4,7 @@
 import shutil
 import glob
 import pandas as pd
-from cmi.stages.create_network import create_network #, get_TFs_data, get_targets_data, get_regulators, get_master_regulators
+from crgem.stages.create_network import create_network 
 
 
 artefacts_path = "./test_dump"

tests/unittest/stages/test_functional_analysis.py

@@ -4,8 +4,8 @@
 import shutil
 import os
 import filecmp
-from cmi.stages.functional_analysis import functional_analysis
-from cmi.common import clean_up
+from crgem.stages.functional_analysis import functional_analysis
+from crgem.common import clean_up
 
 transsynw_genes_file = "/Trrust_Analysis/transsynw_genes.csv"
 signet_genes_file = "/Trrust_Analysis/signet_genes.csv"

tests/unittest/stages/test_generate_hypothesis.py

@@ -3,7 +3,7 @@
 import filecmp
 import os
 import shutil
-from cmi.stages.generate_hypothesis import generate_hypothesis
+from crgem.stages.generate_hypothesis import generate_hypothesis
 print(os.getcwd())
 args = ["start.txt","start_terminal.txt","annotation.txt","HPROGFPM"]
 artefacts_path = os.getcwd() + "/" + "./test_dump"

tests/unittest/stages/test_grn_inference.py

@@ -4,7 +4,7 @@
 import shutil
 import os
 import filecmp
-from cmi.stages.grn_inference import runR
+from crgem.stages.grn_inference import runR
 # from craft.common import clean_up
 
 artefacts_path = "./test_dump"

tests/unittest/stages/test_mechanistic_insights.py

@@ -4,7 +4,7 @@
 import os
 import shutil
 import glob
-from cmi.stages.mechanistic_insights import mechanistic_insights
+from crgem.stages.mechanistic_insights import mechanistic_insights
 
 args = ["start.txt","start_terminal.txt","annotation.txt","HPROGFPM", "HNES"]
 artefacts_path = os.getcwd() + "/" +  "./test_dump"

tests/unittest/stages/test_trrust_analysis.py

@@ -4,7 +4,7 @@
 import shutil
 import os
 import filecmp
-from cmi.stages.trrust_analysis import trrust_analysis
+from crgem.stages.trrust_analysis import trrust_analysis
 
 trrust_db_file = "./data/trrust_rawdata_human.tsv"
 artefacts_path = "./test_dump"