def __init__(self, name, index, read1_n, read2_n, threads, out, other, single_end):
"""
Meka a first construction of object with param by user
:param name:
:param index:
:param reads_dir:
:param threads:
:param out:
:param other:
:param single_end:
"""
self._index_parm = ""
self._reads1_parm = ""
self._reads2_parm = ""
self._threads_parm = ""
self._output_parm = ""
self._command_parm = ""
self._sep = " "
self._name = name
#nIndex = index[(1 + index.rfind('/')):] # (index.rfind('.'))
self._index_name = index # nIndex
self._reads1_name = read1_n
self._reads2_name = read2_n
self._threads_value = threads
self._output_name = out
self._output_type = "--no-convert-bam "
self._other_conf = other
self._paired_end = single_end
self._message = Message()
self.parm_mapp()
def __init__(self):
self._message = Message()
self._file_conf = None
self._name_par = "NAME"
self._replic_parm = "REPLIC"
self._group_number_parm = "GROUP_NUMBER"
self._group_name_parm = "GROUP_NAMES"
self._reference_parm = "REFERENCE_GENOME"
self._read_directory_parm = "READS_DIRECTORY"
self._group_directory_parm = "GROUP_DIRECTORIES"
self._paired_end_parm = "PAIRED_END"
self._threads_parm = "THREADS"
self._count_mode_parm = "MODE"
self._annotation_file_parm = "ANOTATION_FILE"
self._annotation_type_parm = "ANOTATION_TYPE"
self._output_parm = "OUTPUT"
self._name = ""
self._replic = []
self._group_number = 0
self._group_name = []
self._reference = ""
self._read_directory = ""
self._group_directory = []
self._paired_end = False
self._threads = 0
self._count_mode = ""
self._annotation_file = ""
self._annotation_type = ""
self._output = ""
def __init__(self, count):
"""
Test the doc of constructor class
:param count:
"""
assert isinstance(count, CountVo)
self._counter = count
self.message = Message()
def __init__(self, count, group, repl, out):
"""
Inite object Ebseq
:param count:
:param group:
:param repl:
:param out:
"""
self._table_count = count
self._groups_name = group
self._replic = repl
self._output = out
self._message = Message()
self._exp_column = 1
self._exp = "DE"
def __init__(self, count, group, repl, out):
"""
Define the NOISeq object
:param count:
:param group:
:param repl:
:param out:
"""
self._table_count = count
self._groups_name = group
self._replic = repl
self._output = out
self._message = Message()
self._likelihood_column = len(group) + 3
self._likelihood = 0.95
def __init__(self, count, group, repl, out):
"""
Inite object Ebseq
:param count:
:param group:
:param repl:
:param out:
"""
self._table_count = count
self._groups_name = group
self._replic = repl
self._output = out
self._message = Message()
self._logfc_column = 2
self._pvalue_column = 5
self._logfc = 2
self._pvalue = 0.05
def __init__(self, count, group, repl, out):
"""
Define the edgeR object
:param count:
:param group:
:param repl:
:param out:
"""
self._table_count = count
self._groups_name = group
self._replic = repl
self._output = out
self._message = Message()
self._logfc_column = 6
self._pvalue_column = 7
self._pvalue = 0.05
self._logfc = 2
def __init__(self, count, group, repl, out):
"""
Define the edgeR object
:param count:
:param group:
:param repl:
:param out:
"""
self._table_count = count
self._groups_name = group
self._replic = repl
self._output = out
self._message = Message()
self._likelihood_column = 2 + len(group) * repl
self._fdr_de_column = 4 + len(group) * repl
self._likelihood = 0.95
self._fdr = 0.1
def __init__(self, count, group, repl, out):
"""
Inite object Ebseq
:param count:
:param group:
:param repl:
:param out:
"""
robjects.r['options'](warn=-1)
self._table_count = count
self._groups_name = group
self._replic = repl
self._output = out
self._class = '"Two class unpaired"'
self._message = Message()
self._fd_column = 4
self._qvalue_column = 5
self._qvalue = 1
self._fd = 2
def __init__(self):
self._exp_dao = None
self._reference = None
self._transcript = False
self._count = None
self._expression = None
self._mapp_bo = None
self.message = Message()
self._fastq = []
self._out_mapp = []
self._count_table = []
self._merged_table_out = None
self._edger = None
self._bayseq = None
self._deseq = None
self._noiseq = None
self._ebseq = None
self._samseq = None
self._limmavoom = None
def __init__(self, mapp):
assert isinstance(mapp, MappVo)
self._map_vo = mapp
self._reads_file = []
self.message = Message()