parser.add_argument("--sample_id",
type=str,
default=None,
help="Sample id to run MAGeCK on")
parser.add_argument("--v10",
type=str,
default='',
help="Data set label")
args = parser.parse_args()
inputs_dir = 'input_files'
if not os.path.isdir(inputs_dir): os.makedirs(inputs_dir)
# Load the specification of samples to include
LOG.info('Loading sample specification')
sample_spec, ctrl_spec, sample_num_reps = createSampleSpec(args.countfile, args.replicatefile, args.rep_hdr,
args.sample_hdr, args.common_ctrl_sample, args.ctrl_sample_hdr)
# Load the mappings from guides to genes
LOG.info('Loading gene mappings')
gene_spec = createGeneSpec(args.guidemappingfile, args.sgrna_hdr, args.gene_hdr)
# Sample not specified: re-call self for all samples
if args.sample_id is None:
for sample_id in ctrl_spec:
if ctrl_spec[sample_id] == sample_id: continue
cmd = py_cmd + ' ' + ' '.join(sys.argv) + ' --sample_id="%s"' % sample_id
os.system(cmd)
#Sample specified - run MAGeCK
else:
sample_id = args.sample_id
from jacks.infer import LOG, inferJACKSGene
LOG.setLevel(logging.WARNING)
if len(sys.argv) != 8 and len(sys.argv) != 9:
print('Usage: sample_jacks_screen.py condensed_input test_line num_replicates(-1 for all) num_celllines(-1 for all) outfile num_samples num_guides(-1 for all) job_idx\n')
print('where, condensed_input = countfile#replicatefile:rep_hdr:sample_hdr:ctrl_sample_or_hdr#guidemappingfile:sgrna_hdr:gene_hdr#ctrl_genes(can be blank)')
else:
#Minimial checks on this, as this is for a script that is intended for use internally only
condensed_input = sys.argv[1]
countfile, replicatestuff, grnastuff, ctrl_genes = condensed_input.split('#')
replicatefile, rep_hdr, sample_hdr, ctrl_sample_or_hdr = replicatestuff.split(':')
guidemappingfile, sgrna_hdr, gene_hdr = grnastuff.split(':')
ctrl_sample_hdr = ctrl_sample_or_hdr if ctrl_sample_or_hdr == 'Control' else None
sample_spec, ctrl_spec, sample_num_reps = createSampleSpec(countfile, replicatefile, rep_hdr, sample_hdr, ctrl_sample_or_hdr, ctrl_sample_hdr)
gene_spec = createGeneSpec(guidemappingfile, sgrna_hdr, gene_hdr)
test_celllines = [sample_id for sample_id in ctrl_spec if ctrl_spec[sample_id] != sample_id]
ctrl_geneset = readControlGeneset(ctrl_genes) if ctrl_genes is not '' else set()
normtype = 'median'
test_line = sys.argv[2]
num_replicates = eval(sys.argv[3])
num_celllines = eval(sys.argv[4])
outfile = sys.argv[5]
num_samples = eval(sys.argv[6])
num_guides = eval(sys.argv[7])
if len(sys.argv) == 9: job_idx = sys.argv[8]
else: job_idx = os.environ['LSB_JOBINDEX']