def process(self):
# Reduce inputs to only first element
if hasattr(self.input_dir, '__iter__'):
self.input_dir = self.input_dir[0]
self.input_dir = os.path.join(self.input_dir, "Data/Intensities/BaseCalls/")
if type(self.sample_sheet) == list:
if len(self.sample_sheet) > 1:
raise Exception('Too many sample sheet files: %s' % ','.join(self.sample_sheet))
else:
self.sample_sheet = self.sample_sheet[0]
ss = SampleSheet(self.sample_sheet)
mask_length, double_idx = ss.get_mask_length()
if double_idx:
self.use_base_mask = "y*,I{0},I{0},Y*".format(mask_length)
else:
self.use_base_mask = "y*,I{0},Y*".format(mask_length)
self.use_base_mask = str(self.use_base_mask)
super(CasavaDemux, self).process()
prj_dir = os.path.join(self.output_dir, 'Project_' + self.meta['pipeline']['project_name'])
self.output_files = utils.find(prj_dir, "*.fastq.gz")
#set the metadata
self.meta['job']['sample_id'] = []
sample_ids = ss.get_sample_ids()
for output_file in self.output_files:
for sample_id in sample_ids:
if os.path.basename(output_file).startswith("%s_" % sample_id):
self.meta['job']['sample_id'].append(sample_id)
break
def process(self):
# Reduce inputs to only first element
if hasattr(self.input_dir, '__iter__'):
self.input_dir = self.input_dir[0]
if not self.input_dir.endswith('/'):
self.input_dir += '/'
(parent_dir, flowcell_dir) = os.path.split(os.path.dirname(self.input_dir))
parsed = re.search(r'''(?P<DATE>\d{6})_
(?P<HISEQ_SN>\w{6})_
(?P<RUN_COUNT>\d{4})_
(?P<FC_POS>[AB])
(?P<FC_ID>.*$)''', flowcell_dir, re.X)
ss = SampleSheet(os.path.join(self.input_dir, 'SampleSheet.csv'))
ss_validated = os.path.join(self.output_dir, 'sample_sheet_validated.csv')
project_name = ss.get_project_name() or 'DefaultProject'
run_desc = 'Flowcell %s on %s/%s' % (parsed.group('FC_ID'),
os.path.basename(parent_dir),
parsed.group('FC_POS'))
self.meta.update({
'pipeline': {
'date' : parsed.group('DATE'),
'descr' : run_desc,
'fc_id' : parsed.group('FC_ID'),
'fc_pos' : parsed.group('FC_POS'),
'hiseq' : os.path.basename(parent_dir),
'hiseq_sn' : parsed.group('HISEQ_SN'),
'project_name' : project_name,
'run_count' : int(parsed.group('RUN_COUNT')),
'nfiles' : ss.get_lines_count()
}
})
ss_validated = ss.validate(project_name, ss_validated)
self.output_files = [ss_validated]
def create(sample_sheet, input_dir, output_dir=None, output_file_name=None):
"""
Crete a file of file names and return the path to it
Args:
sample_sheet:
full path to the sample sheet
input_dir:
path to the directory containing the input files
output_file:
name of the output fofn. If is not specified the name
"""
if not os.path.exists(sample_sheet):
raise Exception("input error: parameter `sample_sheet` %s does not exist" % sample_sheet)
if not os.path.exists(input_dir):
raise Exception("input error: parameter `input_dir` %s does not exist" % sample_sheet)
print("*********************************")
print("sample_sheet: %s" % os.path.abspath(sample_sheet))
print("input_dir: %s" % os.path.abspath(input_dir))
print("*********************************")
#set default name of the output fofn
if not output_file_name:
output_file_name = os.path.basename(sample_sheet).rsplit(".", 1)[0] + "_fofn.csv"
if not output_dir:
output_dir = os.path.dirname(sample_sheet)
output_file = os.path.join(output_dir, output_file_name)
with open(output_file, 'w') as f_fofn:
ss = SampleSheet(sample_sheet)
sample_id_list = ss.get_sample_ids()
for sample_id in sample_id_list:
print("*********************************")
print "sample_id : %s" %sample_id
for root, dirs, file_list in os.walk(input_dir):
#group the files by sample id and read number
r1_files = [
os.path.join(root, file_name) for file_name in file_list if (
'%s_'%sample_id in file_name and Fofn.r1_regex.search(file_name)
)
]
r2_files = [
os.path.join(root, file_name) for file_name in file_list if (
'%s_'%sample_id in file_name and Fofn.r2_regex.search(file_name)
)
]
r1_file = ""
r2_file = ""
if r1_files:
for r1_file in r1_files:
#filter the R2 files that match the R1 file base
r2_matchs = [
r2_file for r2_file in r2_files if (
Fofn.r1_regex.search(r1_file).group(1) in r2_file)
]
if r2_matchs:
Fofn._write_record(f_fofn, r1_file, r2_matchs[0], sample_id)
else:
if r2_files:
print("No R2 found for sample Id %s" % sample_id)
Fofn._write_record(f_fofn, r1_file, '', sample_id)
else:
if r2_files:
for r2_file in r2_files:
Fofn._write_record(f_fofn, r1_file, r2_file, sample_id)
return output_file
def create(sample_sheet,
input_dir,
output_dir=None,
output_file_name=None):
"""
Crete a file of file names and return the path to it
Args:
sample_sheet:
full path to the sample sheet
input_dir:
path to the directory containing the input files
output_file:
name of the output fofn. If is not specified the name
"""
if not os.path.exists(sample_sheet):
raise Exception(
"input error: parameter `sample_sheet` %s does not exist" %
sample_sheet)
if not os.path.exists(input_dir):
raise Exception(
"input error: parameter `input_dir` %s does not exist" %
sample_sheet)
print("*********************************")
print("sample_sheet: %s" % os.path.abspath(sample_sheet))
print("input_dir: %s" % os.path.abspath(input_dir))
print("*********************************")
#set default name of the output fofn
if not output_file_name:
output_file_name = os.path.basename(sample_sheet).rsplit(
".", 1)[0] + "_fofn.csv"
if not output_dir:
output_dir = os.path.dirname(sample_sheet)
output_file = os.path.join(output_dir, output_file_name)
with open(output_file, 'w') as f_fofn:
ss = SampleSheet(sample_sheet)
sample_id_list = ss.get_sample_ids()
for sample_id in sample_id_list:
print("*********************************")
print "sample_id : %s" % sample_id
for root, dirs, file_list in os.walk(input_dir):
#group the files by sample id and read number
r1_files = [
os.path.join(root, file_name)
for file_name in file_list
if ('%s_' % sample_id in file_name
and Fofn.r1_regex.search(file_name))
]
r2_files = [
os.path.join(root, file_name)
for file_name in file_list
if ('%s_' % sample_id in file_name
and Fofn.r2_regex.search(file_name))
]
r1_file = ""
r2_file = ""
if r1_files:
for r1_file in r1_files:
#filter the R2 files that match the R1 file base
r2_matchs = [
r2_file for r2_file in r2_files
if (Fofn.r1_regex.search(r1_file).group(1) in
r2_file)
]
if r2_matchs:
Fofn._write_record(f_fofn, r1_file,
r2_matchs[0], sample_id)
else:
if r2_files:
print("No R2 found for sample Id %s" %
sample_id)
Fofn._write_record(f_fofn, r1_file, '',
sample_id)
else:
if r2_files:
for r2_file in r2_files:
Fofn._write_record(f_fofn, r1_file, r2_file,
sample_id)
return output_file
