if __name__ == '__main__' :
TERM_ESCAPE = True
try :
pipeline_args = {}
# herro
announce('ChIPSeq Experiment Pipeline Script Generator')
print textwrap.fill(start_text)
opts, args = parser.parse_args(sys.argv[1:])
if len(args) > 0 :
warn("Arguments were passed, but this script doesn't accept any arguments, rudely ignoring them...\n")
# this dictionary will be used to generate a JSON formatted file with
# all the relevant settings for the pipeline
json_dict = {}
############################################################################
# name of the experiment
############################################################################
def_path = os.path.basename(os.getcwd())
exp_name = input('Experiment name',def_path)
exp_name = exp_name.replace(' ','_') # shhhhhhhh...
json_dict['experiment name'] = exp_name
json_dict['analysis path'] = os.getcwd()
if __name__ == '__main__' :
TERM_ESCAPE = True
try :
pipeline_args = [] # list of (arg_key,arg_val) tuples
# herro
announce('ChIP-Seq Experiment Read Alignment Pipeline Script Generator')
print textwrap.fill(start_text)
opts, args = parser.parse_args(sys.argv[1:])
if len(args) > 0 :
warn("Arguments were passed, but this script doesn't accept any arguments, rudely ignoring them...\n")
# this dictionary will be used to generate a JSON formatted file with
# all the relevant settings for the pipeline
json_dict = {}
modules_list = []
############################################################################
# get settings
############################################################################
global_tool_settings = get_global_tool_settings()
local_tool_settings = get_local_tool_settings()
#valid_tool_settings = global_tool_settings.keys() + local_tool_settings.keys()
all_tool_settings = {}
all_tool_settings.update(global_tool_settings)
all_tool_settings.update(local_tool_settings)
# filter the records
pass_recs = []
for peak in peaks :
# test each of the fields, if any one fails skip the record
if not all([c(int(peak['length'])) for c in field_filters['length']]) or \
not all([c(int(peak['tags'])) for c in field_filters['tags']]) or \
not all([c(10**(float(peak['-10*log10(pvalue)'])/-10)) for c in field_filters['pvalue']]) or \
not all([c(float(peak['fold_enrichment'])) for c in field_filters['fold_enrichment']]) or \
not all([c(float(peak['FDR(%)'])) for c in field_filters['fdr']]) :
continue
else :
pass_recs.append([peak[k] for k in MACSOutput.FIELD_NAMES])
if len(pass_recs) == 0 :
warn('WARNING: no records remain after filtering\n')
sys.exit(1)
# sorting
if opts.sort_by :
pass_recs.sort(key=_sort_keys[opts.sort_by],reverse=opts.sort_dir != 'ASCEND')
# top records
num_recs = len(pass_recs) if not opts.top else min(len(pass_recs),opts.top)
# construct the summary string
filters_str = 'none' if len(opts.filters) == 0 else ', '.join(opts.filters)
sort_str = 'original order' if not opts.sort_by else opts.sort_by+', '+opts.sort_dir
shuffled_str = str(opts.shuffle)
summary = summary_str%{'macs_fn':args[0],'num_recs':num_recs,
'filters':filters_str,
