def __init__(self, command_line_args = None, configuration_dictionary = None):
self.args = command_line_args
self.general_config_dict = configuration_dictionary
self.known_header_list = C.csv_header_list
self.pipeline_run_items = C.pipeline_run_items
self.primer_suites = self.convert_primer_suites(C.primer_suites)
self.dna_regions = C.dna_regions
self.data_object = {}
self.data_object['general'] = {}
self.warn_msg = """\n\tThe config File seems to be okay. If the items above look correct
then press 'c' to continue the pipeline\n"""
self.res_headers = []
self.env = {}
self.utils = PipelneUtils()
def __init__(self, runobj = None):
self.utils = PipelneUtils()
self.runobj = runobj
self.run_keys = self.runobj.run_keys
self.rundate = self.runobj.run
try:
self.use_cluster = self.runobj.use_cluster
except:
self.use_cluster = True
self.chg_suffix = ".chg"
self.chimeras_suffix = ".chimeras"
self.ref_suffix = ".db"
self.denovo_suffix = ".txt"
self.nonchimeric_suffix = "." + C.nonchimeric_suffix #".nonchimeric.fa"
self.chimeric_suffix = ".chimeric.fa"
self.base_suffix = "unique" + self.chimeras_suffix
try:
if self.runobj.lane_name:
lane_name = self.runobj.lane_name
else:
lane_name = ''
except:
lane_name = ''
if self.runobj.vamps_user_upload:
site = self.runobj.site
dir_prefix = self.runobj.user + '_' + self.runobj.run
self.dirs = Dirs(self.runobj.vamps_user_upload, dir_prefix, self.runobj.platform, lane_name = lane_name, site = site)
self.idx_keys = convert_unicode_dictionary_to_str(json.loads(open(self.runobj.trim_status_file_name,"r").read()))["new_lane_keys"]
self.indir = self.dirs.check_dir(self.dirs.trimming_dir)
self.outdir = self.dirs.check_dir(self.dirs.chimera_dir)
else:
site = ''
dir_prefix = self.runobj.run
self.dirs = Dirs(self.runobj.vamps_user_upload, dir_prefix, self.runobj.platform, lane_name = lane_name, site = site)
self.indir = self.dirs.check_dir(self.dirs.reads_overlap_dir)
self.outdir = self.dirs.check_dir(self.dirs.chimera_dir)
# self.usearch_cmd = C.usearch_cmd
self.usearch_cmd = C.usearch6_cmd
#self.abskew = C.chimera_checking_abskew
self.refdb = C.chimera_checking_refdb_6
self.its_refdb = C.chimera_checking_its_refdb_6
self.input_file_names = self.make_chimera_input_illumina_file_names()
def __init__(self, runobj):
self.utils = PipelneUtils()
self.runobj = runobj
self.out_files = {}
self.id_dataset_idx = {}
self.in_file_path = self.runobj.input_dir
if self.runobj.vamps_user_upload:
site = self.runobj.site
dir_prefix=self.runobj.user+'_'+self.runobj.run
else:
site = ''
dir_prefix = self.runobj.run
if self.runobj.lane_name:
lane_name = self.runobj.lane_name
else:
lane_name = ''
dirs = Dirs(self.runobj.vamps_user_upload, dir_prefix, self.runobj.platform, lane_name = lane_name, site = site)
self.dirs = dirs
self.out_file_path = dirs.check_dir(dirs.analysis_dir)
self.results_path = dirs.check_dir(dirs.reads_overlap_dir)
self.platform = self.runobj.platform
def __init__(self, runobj=None):
self.utils = PipelneUtils()
self.runobj = runobj
self.run_keys = self.runobj.run_keys
self.rundate = self.runobj.run
try:
self.use_cluster = self.runobj.use_cluster
except:
self.use_cluster = True
self.chg_suffix = ".chg"
self.chimeras_suffix = ".chimeras"
self.ref_suffix = ".db"
self.denovo_suffix = ".txt"
self.nonchimeric_suffix = "." + C.nonchimeric_suffix #".nonchimeric.fa"
self.chimeric_suffix = ".chimeric.fa"
self.base_suffix = "unique" + self.chimeras_suffix
self.cluster_slots = {
"grendel": [12, 8],
"cricket": [40],
"cluster5": [32]
}
try:
if self.runobj.lane_name:
lane_name = self.runobj.lane_name
else:
lane_name = ''
except:
lane_name = ''
if self.runobj.vamps_user_upload:
os.environ['SGE_ROOT'] = '/opt/sge'
os.environ['SGE_CELL'] = 'grendel'
path = os.environ['PATH']
os.environ['PATH'] = '/opt/sge/bin/lx24-amd64:' + path
site = self.runobj.site
dir_prefix = self.runobj.user + '_' + self.runobj.run
self.dirs = Dirs(self.runobj.vamps_user_upload,
dir_prefix,
self.runobj.platform,
lane_name=lane_name,
site=site)
self.idx_keys = convert_unicode_dictionary_to_str(
json.loads(
open(self.runobj.trim_status_file_name,
"r").read()))["new_lane_keys"]
self.analysis_dir = self.dirs.check_dir(self.dirs.analysis_dir)
self.indir = self.dirs.check_dir(self.dirs.trimming_dir)
self.outdir = self.dirs.check_dir(self.dirs.chimera_dir)
self.gast_dir = self.dirs.check_dir(self.dirs.gast_dir)
else:
site = ''
dir_prefix = self.runobj.run
self.dirs = Dirs(self.runobj.vamps_user_upload,
dir_prefix,
self.runobj.platform,
lane_name=lane_name,
site=site)
self.indir = self.dirs.check_dir(self.dirs.reads_overlap_dir)
self.outdir = self.dirs.check_dir(self.dirs.chimera_dir)
# self.usearch_cmd = C.usearch_cmd
self.usearch_cmd = C.usearch6_cmd
if self.utils.is_local():
self.usearch_cmd = C.usearch6_cmd_local
#self.abskew = C.chimera_checking_abskew
self.refdb = C.chimera_checking_refdb
if self.utils.is_local():
self.refdb_local = C.chimera_checking_refdb_local
self.its_refdb = C.chimera_checking_its_refdb
self.input_file_names = self.make_chimera_input_illumina_file_names()
