def main(args,args_from_ui=None):
'''
the main entry point into dose_analysis_tool
'''
# register the tool with tool ops
work_dir = tool_ops.register_tool('dose_analysis_tool', args,
start_path = args.out,
args_from_ui = args_from_ui)
#build_SC(args,work_dir)
#build_query(args,work_dir)
if args.probe:
build_probe_curves(args,work_dir)
if args.result:
analyze_query(args,work_dir)
def main(args,args_from_ui=None):
'''
the main entry point into dose_analysis_tool
'''
# register the tool with tool ops
work_dir = tool_ops.register_tool('dose_analysis_tool', args,
start_path = args.out,
args_from_ui = args_from_ui)
#metics based on gctx input
build_SC(args,work_dir)
template_heatmap(args,work_dir)
if args.probe:
build_probe_curves_and_summary(args,work_dir)
#query based functions
if args.query:
build_query(args,work_dir)
if args.result or args.resultDir:
analyze_query(args,work_dir)
def main(args, args_from_ui=None):
'''
the main entry point into dose_analysis_tool
'''
# register the tool with tool ops
work_dir = tool_ops.register_tool('dose_analysis_tool',
args,
start_path=args.out,
args_from_ui=args_from_ui)
#make signature for each dose
fup = os.path.join(work_dir, 'tmp_up_list.gmt')
fdn = os.path.join(work_dir, 'tmp_dn_list.gmt')
#fup = '/xchip/cogs/hogstrom/analysis/scratch/tmp_up_list.gmt'
#fdn = '/xchip/cogs/hogstrom/analysis/scratch/tmp_dn_list.gmt'
open(fup, 'w') #overwrite existing grp file
open(fdn, 'w') #overwrite existing grp file
n_edge = 50
db = gct.GCT()
#db.read(gctfile)
db.read(args.res)
cids = db.get_cids()
pertIDs = [x.split(':')[1] for x in cids]
doses = [float(x.split(':')[2]) for x in cids]
perts = db.get_column_meta('pert_desc')
probes = db.get_rids()
cellLs = db.get_column_meta('cell_id')
timePs = db.get_column_meta('pert_time')
mtrx = db.matrix #matrix of data from gct file
#loop through each column of data
for i, pertID in enumerate(pertIDs):
profile = mtrx[:, i]
n_prof = len(profile)
iprofile = profile.argsort() #indices that sort array
iprofile = iprofile[::-1] #switch indicies to decend
sprofile = profile[iprofile]
itop = iprofile[0:(n_edge)]
ibot = iprofile[-n_edge:n_prof]
col_name = perts[i] + '_' + str(
doses[i]) + 'um_' + cellLs[i] + '_' + timePs[i]
ptop = []
pbot = []
for j, it in enumerate(itop):
ptop.append(probes[it]) #make probe id list
for j, ip in enumerate(ibot):
pbot.append(probes[ip]) #make probe id list
#write to gmt list
with open(fup, 'a') as f:
f.write(col_name + '\t' + col_name + '\t')
for pt in ptop:
f.write(pt + '\t')
f.write('\n')
with open(fdn, 'a') as f:
f.write(col_name + '\t' + col_name + '\t')
for pb in pbot:
f.write(pb + '\t')
f.write('\n')
#python system call
os.chdir(work_dir)
cmd = 'rum -q local query_tool --uptag ' + fup + ' --dntag ' + fdn + ' --metric eslm'
os.system(cmd)