def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if argv is None: argv = sys.argv # setup command line parser parser = E.OptionParser(version="%prog version: $Id$", usage=globals()["__doc__"]) parser.add_option("-t", "--test", dest="test", type="string", help="supply help") parser.add_option("--fcs-directory", dest="fcs_dir", type="string", help="path to directory containing .fcs files" " for processsing") parser.add_option("--output-format", dest="out_format", type="choice", choices=("summary", "intensity"), help="output either" " summary of intensities or raw intensity data") parser.add_option("--summary-stats", dest="stats", type="choice", choices=("fano", "mean", "std", "var", "median", "geometric", "regress"), help="summary statistics to output if " "out_format == summary") parser.add_option("--gating-strategy", dest="gates", type="string", help=".tsv of gating strategy. See docs for details") parser.add_option( "--compensation-matrix", dest="comp_matrix", type="string", help="text file containing the compensation/spillover matrix") parser.add_option("--cell-type", dest="cell_type", type="string", help="description of cell type gene expression " "is measured on. Will be added to output file name") parser.add_option("--panel-id", dest="panel", type="string", help="ID for marker panel") parser.add_option("--output-directory", dest="out_dir", type="string", help="output directory path for files") parser.add_option( "--fileset-identifier", dest="fileset_id", type="string", help="unique identifier for sets of files/samples processed " "together. Useful for assigning to batches for processing") parser.add_option("--database", dest="database", type="string", help="SQLite database to write results to ") # add common options (-h/--help, ...) and parse command line (options, args) = E.Start(parser, argv=argv) E.info("Processing data for %s in panel %s" % (options.cell_type, options.panel)) if options.cell_type == "CD4_Tmem" and options.panel == "P3": P52.get_cd4_Tmem_panel3(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD8_Tmem" and options.panel == "P3": P52.get_cd8_Tmem_panel3(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD4_Tnaive" and options.panel == "P3": P52.get_cd4_naive_panel3(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD8_Tnaive" and options.panel == "P3": P52.get_cd8_naive_panel3(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD4_Tcell" and options.panel == "P1": P52.get_cd4_tcells_panel1(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD8_Tcell" and options.panel == "P1": P52.get_cd8_tcells_panel1(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "DN_Tcell" and options.panel == "P1": P52.get_dn_tcells_panel1(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "DP_Tcell" and options.panel == "P1": P52.get_dp_tcells_panel1(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD4_Tcell" and options.panel == "P2a": P52.get_cd4_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD4_Tcell" and options.panel == "P2b": P52.get_cd4_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD8_Tcell" and options.panel == "P2a": P52.get_cd8_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD8_Tcell" and options.panel == "P2b": P52.get_cd8_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "DN_Tcell" and options.panel == "P2a": P52.get_dn_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "DN_Tcell" and options.panel == "P2b": P52.get_dn_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "DP_Tcell" and options.panel == "P2a": P52.get_dp_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "DP_Tcell" and options.panel == "P2b": P52.get_dp_tcells_panel2(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) # elif options.cell_type == "early_NK" and options.panel == "P4": # P52.get_early_nkcells_panel4(fcs_dir=options.fcs_dir, # out_dir=options.out_dir, # comp_matrix=options.comp_matrix, # panel=options.panel, # setid=options.fileset_id, # cell_subset=options.cell_type, # db=options.database) # elif options.cell_type == "terminal_NK" and options.panel == "P4": # P52.get_terminal_nkcells_panel4(fcs_dir=options.fcs_dir, # out_dir=options.out_dir, # comp_matrix=options.comp_matrix, # panel=options.panel, # setid=options.fileset_id, # cell_subset=options.cell_type, # db=options.database) # elif options.cell_type == "mature_NK" and options.panel == "P4": # P52.get_mature_nkcells_panel4(fcs_dir=options.fcs_dir, # out_dir=options.out_dir, # comp_matrix=options.comp_matrix, # panel=options.panel, # setid=options.fileset_id, # cell_subset=options.cell_type, # db=options.database) elif options.cell_type == "NKT_early" and options.panel == "P5": P52.get_early_nktcells_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "NKT_naive" and options.panel == "P5": P52.get_naive_nktcells_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "NKT_terminal" and options.panel == "P5": P52.get_terminal_nktcells_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "NKT_effector" and options.panel == "P5": P52.get_effector_nktcells_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "Vd1_Tcells" and options.panel == "P5": P52.get_Vd1_tcells_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "Vd2p_Vg9dim" and options.panel == "P5": P52.get_Vd2_vg9dim_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "Vd2n_Vg9p" and options.panel == "P5": P52.get_Vd2n_vg9p_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "hemat_SCs" and options.panel == "P5": P52.get_hemat_SC_panel5(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "immature_Bcell" and options.panel == "P6": P52.get_immature_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "mature_Bcell" and options.panel == "P6": P52.get_mature_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "memory_Bcell" and options.panel == "P6": P52.get_memory_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "naive_Bcell" and options.panel == "P6": P52.get_naive_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "IgA_Bmem" and options.panel == "P6": P52.get_IgA_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "IgG_Bmem" and options.panel == "P6": P52.get_IgG_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "IgM_Bmem" and options.panel == "P6": P52.get_IgM_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "IgE_Bmem" and options.panel == "P6": P52.get_IgE_Bcells_panel6(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "monocytes" and options.panel == "P7": P52.get_monocytes_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "M_dendritic" and options.panel == "P7": P52.get_myeloid_DC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "DC_cd123cd11c" and options.panel == "P7": P52.get_cd123cd11c_DC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "P_dendritic" and options.panel == "P7": P52.get_plasmacytoid_DC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD8_APCs" and options.panel == "P7": P52.get_CD8_APC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD4_APCs" and options.panel == "P7": P52.get_CD4_APC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD1cneg_mDC" and options.panel == "P7": P52.get_CD1cneg_mDC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "Inflam_DC" and options.panel == "P7": P52.get_inflammatory_DC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) elif options.cell_type == "CD16neg_DC" and options.panel == "P7": P52.get_CD16neg_DC_panel7(fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database) else: outfile = "%s/%s-%s-%s.tsv" % (options.out_dir, options.fileset_id, options.panel, options.cell_type) P.touch(outfile) # write footer and output benchmark information. E.Stop()
def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if argv is None: argv = sys.argv # setup command line parser parser = E.OptionParser(version="%prog version: $Id$", usage=globals()["__doc__"]) parser.add_option("-t", "--test", dest="test", type="string", help="supply help") parser.add_option( "--fcs-directory", dest="fcs_dir", type="string", help="path to directory containing .fcs files" " for processsing", ) parser.add_option( "--output-format", dest="out_format", type="choice", choices=("summary", "intensity"), help="output either" " summary of intensities or raw intensity data", ) parser.add_option( "--summary-stats", dest="stats", type="choice", choices=("fano", "mean", "std", "var", "median", "geometric", "regress"), help="summary statistics to output if " "out_format == summary", ) parser.add_option( "--gating-strategy", dest="gates", type="string", help=".tsv of gating strategy. See docs for details" ) parser.add_option( "--compensation-matrix", dest="comp_matrix", type="string", help="text file containing the compensation/spillover matrix", ) parser.add_option( "--cell-type", dest="cell_type", type="string", help="description of cell type gene expression " "is measured on. Will be added to output file name", ) parser.add_option("--panel-id", dest="panel", type="string", help="ID for marker panel") parser.add_option("--output-directory", dest="out_dir", type="string", help="output directory path for files") parser.add_option( "--fileset-identifier", dest="fileset_id", type="string", help="unique identifier for sets of files/samples processed " "together. Useful for assigning to batches for processing", ) parser.add_option("--database", dest="database", type="string", help="SQLite database to write results to ") # add common options (-h/--help, ...) and parse command line (options, args) = E.Start(parser, argv=argv) E.info("Processing data for %s in panel %s" % (options.cell_type, options.panel)) if options.cell_type == "CD4_Tmem" and options.panel == "P3": P52.get_cd4_Tmem_panel3( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD8_Tmem" and options.panel == "P3": P52.get_cd8_Tmem_panel3( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD4_Tnaive" and options.panel == "P3": P52.get_cd4_naive_panel3( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD8_Tnaive" and options.panel == "P3": P52.get_cd8_naive_panel3( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD4_Tcell" and options.panel == "P1": P52.get_cd4_tcells_panel1( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD8_Tcell" and options.panel == "P1": P52.get_cd8_tcells_panel1( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "DN_Tcell" and options.panel == "P1": P52.get_dn_tcells_panel1( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "DP_Tcell" and options.panel == "P1": P52.get_dp_tcells_panel1( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD4_Tcell" and options.panel == "P2a": P52.get_cd4_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD4_Tcell" and options.panel == "P2b": P52.get_cd4_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD8_Tcell" and options.panel == "P2a": P52.get_cd8_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD8_Tcell" and options.panel == "P2b": P52.get_cd8_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "DN_Tcell" and options.panel == "P2a": P52.get_dn_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "DN_Tcell" and options.panel == "P2b": P52.get_dn_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "DP_Tcell" and options.panel == "P2a": P52.get_dp_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "DP_Tcell" and options.panel == "P2b": P52.get_dp_tcells_panel2( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) # elif options.cell_type == "early_NK" and options.panel == "P4": # P52.get_early_nkcells_panel4(fcs_dir=options.fcs_dir, # out_dir=options.out_dir, # comp_matrix=options.comp_matrix, # panel=options.panel, # setid=options.fileset_id, # cell_subset=options.cell_type, # db=options.database) # elif options.cell_type == "terminal_NK" and options.panel == "P4": # P52.get_terminal_nkcells_panel4(fcs_dir=options.fcs_dir, # out_dir=options.out_dir, # comp_matrix=options.comp_matrix, # panel=options.panel, # setid=options.fileset_id, # cell_subset=options.cell_type, # db=options.database) # elif options.cell_type == "mature_NK" and options.panel == "P4": # P52.get_mature_nkcells_panel4(fcs_dir=options.fcs_dir, # out_dir=options.out_dir, # comp_matrix=options.comp_matrix, # panel=options.panel, # setid=options.fileset_id, # cell_subset=options.cell_type, # db=options.database) elif options.cell_type == "NKT_early" and options.panel == "P5": P52.get_early_nktcells_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "NKT_naive" and options.panel == "P5": P52.get_naive_nktcells_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "NKT_terminal" and options.panel == "P5": P52.get_terminal_nktcells_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "NKT_effector" and options.panel == "P5": P52.get_effector_nktcells_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "Vd1_Tcells" and options.panel == "P5": P52.get_Vd1_tcells_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "Vd2p_Vg9dim" and options.panel == "P5": P52.get_Vd2_vg9dim_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "Vd2n_Vg9p" and options.panel == "P5": P52.get_Vd2n_vg9p_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "hemat_SCs" and options.panel == "P5": P52.get_hemat_SC_panel5( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "immature_Bcell" and options.panel == "P6": P52.get_immature_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "mature_Bcell" and options.panel == "P6": P52.get_mature_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "memory_Bcell" and options.panel == "P6": P52.get_memory_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "naive_Bcell" and options.panel == "P6": P52.get_naive_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "IgA_Bmem" and options.panel == "P6": P52.get_IgA_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "IgG_Bmem" and options.panel == "P6": P52.get_IgG_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "IgM_Bmem" and options.panel == "P6": P52.get_IgM_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "IgE_Bmem" and options.panel == "P6": P52.get_IgE_Bcells_panel6( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "monocytes" and options.panel == "P7": P52.get_monocytes_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "M_dendritic" and options.panel == "P7": P52.get_myeloid_DC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "DC_cd123cd11c" and options.panel == "P7": P52.get_cd123cd11c_DC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "P_dendritic" and options.panel == "P7": P52.get_plasmacytoid_DC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD8_APCs" and options.panel == "P7": P52.get_CD8_APC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD4_APCs" and options.panel == "P7": P52.get_CD4_APC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD1cneg_mDC" and options.panel == "P7": P52.get_CD1cneg_mDC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "Inflam_DC" and options.panel == "P7": P52.get_inflammatory_DC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) elif options.cell_type == "CD16neg_DC" and options.panel == "P7": P52.get_CD16neg_DC_panel7( fcs_dir=options.fcs_dir, out_dir=options.out_dir, comp_matrix=options.comp_matrix, panel=options.panel, setid=options.fileset_id, cell_subset=options.cell_type, db=options.database, ) else: outfile = "%s/%s-%s-%s.tsv" % (options.out_dir, options.fileset_id, options.panel, options.cell_type) P.touch(outfile) # write footer and output benchmark information. E.Stop()