Configuration settings

Path settings

The path to IMDA’s input and output files as well as to IMDA’s third party software has to be set manually in settings.py.

Step 1: Open the settings.py with your Python 3.7 environment (IDLE, PyCharm, VS, Spyder,…).
Step 2: Open your cmd on Windows or terminal on Linux, respectively. Enter the following command:

pip install --upgrade -r PATH_TO\requirements.txt

Step 3: Please replace all **PATH_TO_…** with the path on your device.
Step 4: Set your global path for input and output files.
Step 5: Set the path to your input files and to your undetermined files (optional)
Step 6: Set your path to your barcode.txt, which defines barcodes and unique molecular identifiers (UMIs) for all samples and pairs.txt (optional - only if FACS error correction is required). Please find the format descriptions in Format Description or adapt the added sample file in the download example in the Download section.

You can find more information about third party software and the downloads in the section Third party software.

### Third Party Software ###
migec = "java -Xmx8G -jar **PATH_TO_MIGEC**/migec-1.2.9/migec-1.2.9.jar"
mixcr = "java -Xmx8G -jar **PATH_TO_MiXCR**/mixcr-3.0.13/mixcr.jar"
mixcr_library = "--library imgt.202037-1.sv6" #or None
bowtie = "**PATH_TO_BOWTIE2**/bowtie2-2.3.4-mingw-x86_64/bowtie2"
bowtie_library = "**PATH_TO_BOWTIE2_LIBRARY**/TCRPHIXREST/TCRPHIXREST"
vdjtools = "java -Xmx1G -jar **PATH_TO_VDJTools**/vdjtools-1.2.1/vdjtools-1.2.1.jar"

### Path to Folder (defines input and output folder) ###
glob_path = "C:/IMDAtest/"

### Path to Folder with Files ###
in_path = glob_path + "Input_Files/"
undetermined_path = glob_path + "Undetermined_Files/"

### Path to Barcode File (barcodes.txt) and FACS Correction File (pairs) ###
barcode_file = glob_path + "barcodes.txt"
facs_correction_file = glob_path + "pairs.txt"

IMDA Settings

All required methods have to be set True or False.

Step 7: Enter a title for your Run (optional).
Step 8: Please set all do_something-methods True (if required) or False (if not required).
Step 9: Run settings.py.

### Run Informations ###
RUN = "My Title"

### B or T cell chain ###
chain = "TRB"                                   # TRA, TRB, IGH, etc.
species = "hsa"                                 # hsa (or HomoSapiens), mmu (or MusMusculus)

### Set Required Methods True ###
i = initialize.initialize(RUN = RUN,
       glob_path=glob_path,
       in_path=in_path,
       undetermined_path=undetermined_path,
       barcode_file=barcode_file,
       facs_correction_file=facs_correction_file,
       migec=migec,
       mixcr=mixcr,
       chain=chain,
       species=species,
       mixcr_library=mixcr_library,
       bowtie=bowtie,
       bowtie_library=bowtie_library,
       vdjtools=vdjtools,
       do_Bowtie=False,                 # perform undetermined mapping
       do_MIGEC=True,                   # perform demultiplexing and UMI assembling
       do_MiXCR=True,                   # perform gene mapping, clonotype identification and quantification
       do_VDJtools=False,               # perform conversion and calculation of diversity indices (required for SimilarityAnalysis)
       do_FACSCorrection=False,         # perform cell disambiguation after e.g. FACS or magnetic sorting
       do_ContaminationProcessing=False,
       do_ContaminationAnalysis=False,
       do_EvaluateUndetermined=False,
       do_ClonalityAnalysis=False,
       do_DiversityAnalysis=False,
       do_OverlapAnalysis=False,
       do_SimilarityAnalysis=False,
       do_VDJAnalysis=False)