NOTE:
make_features.py didn't like this case_tube_idx (although it must have passed the first time...[in meta db load])
INFO make_features 73 Case: 08-18308, Case_tube_idx: 472, File: Hodgkin_Cases_2008_2013/08-18308/08-18308_Hodgkins-fix.fcs [6 of 11]
/home/local/AMC/hermands/repos/flow_anal/FlowAnal/FCS.py:64: UserWarning: loading FCS as empty because unsupported mode or datatype
warnings.warn("loading FCS as empty because %s" % e)
Skipping FCS /home/local/AMC/ngdavid/clinical_cHL_cases/Hodgkin_Cases_2008_2013/08-18308/08-18308_Hodgkins-fix.fcs because of unknown error related to: <type
'exceptions.AttributeError'>
I see only 3 files in the ML_input HDF5 file ['14-22828', '14-22838', '14-22847'] I don't know if that is correct without seeing what is in FCS_2014/500. If it were a typical day, i would have expected more cases.
Features appear to have extracted properly for these 3 cases and the annotation are correct from annots.txt
Please take a look. I believe I fixed handling and logic.
Tests I ran include: MYELOID:
HODGKIN:
NOTE: make_features.py didn't like this case_tube_idx (although it must have passed the first time...[in meta db load]) INFO make_features 73 Case: 08-18308, Case_tube_idx: 472, File: Hodgkin_Cases_2008_2013/08-18308/08-18308_Hodgkins-fix.fcs [6 of 11] /home/local/AMC/hermands/repos/flow_anal/FlowAnal/FCS.py:64: UserWarning: loading FCS as empty because unsupported mode or datatype warnings.warn("loading FCS as empty because %s" % e) Skipping FCS /home/local/AMC/ngdavid/clinical_cHL_cases/Hodgkin_Cases_2008_2013/08-18308/08-18308_Hodgkins-fix.fcs because of unknown error related to: <type 'exceptions.AttributeError'>