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()
