def __init__(self,
fq1,
adapter3,
path_out=None,
len_min=15,
fq2=None,
**kwargs):
"""Parsing the parameters for reads trimming
support both SE and PE reads
"""
assert isinstance(fq1, str) # process one file
args = args_init(kwargs) # default parameters
# print(args)
args['fq1'] = fq1
args['fq2'] = fq2
args['adapter3'] = adapter3
args['path_out'] = path_out
args['len_min'] = len_min
## validate options
assert is_path(path_out)
if args['cut_to_length'] > 0 and args['cut_to_length'] < len_min:
raise Exception(
'illegal length, --trim-to-length %s --len-min %s' %
(args['cut_to_length'], len_min))
self.kwargs = args # global
def main():
args = args_init(vars(get_args()), align=True) # save as dictionary
# log.info('aaaaa')
# args['align_to_te'] = True
## run alignment
map_bam_list = Alignment(**args).run()
def main():
logging.info('Demultiplexing: start')
args = args_init(vars(get_args()),
demx=True,
trim=False,
align=False,
call_peak=False) # save as dictionary
Demx(**args).run()
logging.info('Delumtiplexing: finish')
def __init__(self, fq1, sample_info, path_out, demx_type='p7', **kwargs):
args1 = args_init(kwargs,
demx=True,
trim=False,
align=False,
call_peak=False)
args2 = {
'fq1': fq1,
'sample_info': sample_info,
'path_out': path_out,
'demx_type': demx_type
}
self.kwargs = {**args1, **args2}
assert is_path(path_out)
def main():
## prepare arguments
args = args_init(vars(get_args()), bam2bw=True)
# print(args)
if isinstance(args['bam'], str):
if isinstance(args['scale'], float):
pass
else:
raise Exception('--bam, --scale, not in the same length')
elif isinstance(args['bam'], list):
if isinstance(args['scale'], list) and len(args['scale']) == 1:
pass
elif isinstance(args['scale'], list) and len(args['bam']) == len(args['scale']):
pass
else:
raise Exception('--bam, --scale, not in the same length')
else:
pass
## functions
bam_files = args.pop('bam', None)
path_out = args.pop('path_out', None)
scale_list = args.pop('scale', None)
if len(scale_list) == 1 and len(bam_files) > 1:
scale_list = scale_list * len(bam_files)
elif len(scale_list) == len(bam_files):
pass
else:
sys.exit('lenght of --scale and -b are not equal')
# scale_list = args.pop('scale', None)
## program
for bam_file in bam_files:
i = bam_files.index(bam_file)
scale = scale_list[i]
## strand
if args['filterRNAstrand'] == 'both':
## forward strand
args['filterRNAstrand'] = 'forward'
bam2bw(bam_file, path_out, scale, **args)
## reverse strand
args['filterRNAstrand'] = 'reverse'
bam2bw(bam_file, path_out, scale, **args)
## reset
args['filterRNAstrand'] = 'both'
else:
bam2bw(bam_file, path_out, scale, **args)
def main():
# args = vars(get_args()) # save as dictionary
args = args_init(vars(get_args()), trim=True, align=False, call_peak=False) # save as dictionary
fq1_files = args.pop('fq1', None) # remove 'fq1'
## update arguments
args_lib = args_default(args['library_type'])
args = {**args, **args_lib}
log.info('trimming start')
## SE mode
if args['fq2'] is None:
for fq1 in fq1_files:
tmp = Trimmer(fq1=fq1, **args).trimmer()
## PE mode
else:
fq2_files = args.pop('fq2', None) # remove 'fq2'
for fq1, fq2 in zip(fq1_files, fq2_files):
tmp = Trimmer(fq1=fq1, fq2=fq2, **args).trimmer()
log.info('trimming finish')
def main():
args = args_init(vars(get_args()), align=True)
if args['design'] is None:
# require -c1, -t1, -g
if args['c1'] is None or args['t1'] is None:
log.error('require --design, or -c1, -t1')
else:
if not supportedGenome(args['genome']):
log.error('genome not supported: {}'.foramt(args['genome']))
run(args)
else:
design = DesignReader(args['design'])
# save to file
design.to_json()
# search dict
d = design.to_dict()
for k in d:
log.info(k)
dict_k = d[k]
args['c1'], args['c2'] = dict_k['control']
args['t1'], args['t2'] = dict_k['treatment']
args['c2'] = args['c2'] if len(args['c2']) > 0 else None
args['t2'] = args['t2'] if len(args['t2']) > 0 else None
args['C'] = dict_k['control_name']
args['T'] = dict_k['treatment_name']
args['genome'] = dict_k['genome']
args['path_out'] = dict_k['path_out']
args['spikein'] = dict_k['spikein']
## supported
if not supportedGenome(args['genome']):
log.info('genome not supported: {}'.format(args['genome']))
continue
run(args)