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davidpng / FCS_Database

Program to scrape an FCS directory of metadata
GNU General Public License v3.0
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FlowAnal

Program to analyze flow cytometry .fcs files

DEV setup

dev/venv.sh

Load HP database meta information (example)

FCS_Database-env/bin/activate

Update version

python setup.py -h

Make .fcs file list

./flowanal.py -v make_FCS_file_list /home/local/AMC/ngdavid/clinical_cHL_cases/ [-n 30]

Make FCS db

./flowanal.py make_FCSmeta_db /home/local/AMC/ngdavid/clinical_cHL_cases/

Make FCS db from archive volume

python flowanal.py make_FCSmeta_db '/mnt/hgfs/archive/' --ex 'archive2' 'Duplicate data' '~snapshot' 'test' 'MISC archive files' 'FC500' --fl 'db/NewFileList.txt'

Export Tube types data

./flowanal.py tube_types -export

Import Tube types data

db/tube_types.tmp ./flowanal.py tube_types -load # Add QC stats ./flowanal.py add_FCSstats_db /home/local/AMC/ngdavid/clinical_cHL_cases/ -tubes Hodgkin Hodgkins # Do something with QC stats ./flowanal.py -v process_FCSstats -tubes Hodgkin Hodgkins --table-format tall [--testing] # Query FCS db for Hodgkins tubes ./flowanal.py query_db --tubes Hodgkins --daterange 2012-01-01 2013-01-01 --outfile db/cases.tmp # Template for querying FCS db and doing something with results ./flowanal.py template-query_do /home/local/AMC/ngdavid/clinical_cHL_cases/ -tubes Hodgkins -dates 2013-1-1 2013-1-10