def check_track_clone_options(parser, options):
options.clones = None
if options.clonefile:
libcommon.check_options_file(options.clonefile)
options.clones = libcommon.read_list(options.clonefile)
if options.track_minfreq > 1.0:
parser.error("--track_minfreq is the proportion, not %, should be < 1")
def check_input_options(parser, options):
if options.indir is None:
raise libcommon.InputError("Please specify input directory.")
libcommon.check_options_dir(options.indir)
if not os.path.exists(options.outdir):
system("mkdir -p %s" % options.outdir)
libcommon.check_options_dir(options.outdir)
if not options.jobTree:
options.jobTree = os.path.join(options.outdir, "jobTree")
options.group2samples = None
options.matched = None
if options.metainfo:
libcommon.check_options_file(options.metainfo)
groups, group2samples, matched = read_group_info(options.metainfo)
options.group2samples = group2samples
options.matched = matched
options.groups = groups
my_analyses = ['diversity', 'similarity', 'clonesize', 'lendist',
'geneusage', 'aausage', 'overlap', 'trackclone',
'prelim', 'db', 'model']
analyses = []
if options.analyses:
analyses = options.analyses.split(',')
if 'all' in analyses:
analyses = my_analyses[:-3]
#if not options.matched:
# analyses.remove('trackclone')
else:
for a in analyses:
if a not in my_analyses:
raise libcommon.InputError("Unknown analysis %s." % a)
#if 'trackclone' in analyses and not options.matched:
# raise libcommon.InputError(("Matched samples are required if " +
# "'trackclone' analysis is specified." +
# " Please modify the metadata file."))
options.analyses = analyses
if options.samout:
samouts = options.samout.split(',')
for samout in samouts:
if samout not in ['fasta', 'txt', 'pickle', 'all']:
raise libcommon.InputError("Unknown sample out format %s." %
samout)
if 'all' in samouts:
options.samout = ['fasta', 'txt', 'pickle']
else:
options.samout = samouts
if 'prelim' in analyses and 'pickle' not in options.samout:
options.samout.append('pickle')
samoutdir = os.path.join(options.outdir, "samples")
for format in options.samout: # e.g: outdir/samples/productive/pickle
dir1 = os.path.join(samoutdir, "productive", format)
system("mkdir -p %s" % dir1)
dir2 = os.path.join(samoutdir, "non_productive", format)
system("mkdir -p %s" % dir2)
drawcommon.check_plot_options(parser, options)
