コード例 #1
0
    def run(self):
        """
		09-08-05
			
			--db_connect()
			--org_short2long()
			--org2tax_id()
			--setup_acc2gene_id()
			if self.new_table
				--create_output_table()
			--parse_input_filename()
		"""
        (conn, curs) = db_connect(self.hostname, self.dbname)
        long_organism = org_short2long(self.organism)
        tax_id_set = Set([org2tax_id(long_organism)])

        MdbId2GeneId_instance = MdbId2GeneId()
        acc2gene_id = MdbId2GeneId_instance.setup_acc2gene_id(
            self.acc_file, tax_id_set)
        if self.new_table:
            self.create_output_table(curs, self.output_table)
        self.parse_input_filename(curs, self.input_filename, self.output_table,  acc2gene_id,\
         org2tax_id(long_organism), self.up_length, self.comment, long_organism, self.type)
        if self.commit:
            curs.execute("end")
コード例 #2
0
ファイル: DatasetsIdExchange.py プロジェクト: polyactis/annot
	def __init__(self, file_list=[], outputdir=None, delimiter='\t', organism='at', mapping_file=None, type=1, debug=0):
		""" 
		09-30-05
		"""
		self.files = file_list
		self.files.sort()
		self.outputdir = outputdir
		self.delimiter = delimiter
		self.organism = org_short2long(organism)
		self.mapping_file = mapping_file
		self.type = int(type)
		self.debug = int(debug)
コード例 #3
0
ファイル: gene_table.py プロジェクト: polyactis/annot
	def __init__(self, dir=None, hostname='zhoudb', dbname='graphdb', schema=None, \
		output_table='gene', orgn='', min_frequency=0, needcommit=0):
		"""
		08-30-05
			add rn to org_short2long
		"""
		self.dir = dir
		self.hostname = hostname
		self.dbname = dbname
		self.schema = schema
		self.output_table = output_table
		self.organism = org_short2long(orgn)
		self.min_frequency = int(min_frequency)
		self.needcommit = int(needcommit)		
コード例 #4
0
ファイル: Schema2Darwin.py プロジェクト: polyactis/annot
	def __init__(self, *arguments):
		"""
		12-01-05
			add running_bit
		2006-09-25 use pattern_table, cluster_bs_table, input_fname
			use *arguments
		"""
		self.hostname, self.dbname, self.schema, self.pattern_table, self.cluster_bs_table, self.input_fname, \
		self.lm_bit, self.acc_cut_off, self.output_dir, self.organism, self.running_bit, self.debug, self.report = arguments
		
		self.organism = org_short2long(self.organism)
		self.acc_cut_off = float(acc_cut_off)
		self.debug = int(debug)
		self.report = int(report)
コード例 #5
0
 def __init__(self, hostname='zhoudb', dbname='graphdb', input_fname=None,\
  matrix_table='transfac.matrix', prom_seq_table='transfac.prom_seq', \
  output_table='graph.gene_id2mt_no_p_value', p_value_cut_off=0.001, organism='hs', \
  commit=0, debug=0, report=0):
     self.hostname = hostname
     self.dbname = dbname
     self.input_fname = input_fname
     self.matrix_table = matrix_table
     self.prom_seq_table = prom_seq_table
     self.output_table = output_table
     self.p_value_cut_off = float(p_value_cut_off)
     self.organism = org_short2long(organism)
     self.commit = int(commit)
     self.debug = int(debug)
     self.report = int(report)
コード例 #6
0
	def __init__(self, hostname='zhoudb', dbname='graphdb', input_fname=None,\
		matrix_table='transfac.matrix', prom_seq_table='transfac.prom_seq', \
		output_table='graph.gene_id2mt_no_p_value', p_value_cut_off=0.001, organism='hs', \
		commit=0, debug=0, report=0):
		self.hostname = hostname
		self.dbname = dbname
		self.input_fname = input_fname
		self.matrix_table = matrix_table
		self.prom_seq_table = prom_seq_table
		self.output_table = output_table
		self.p_value_cut_off = float(p_value_cut_off)
		self.organism = org_short2long(organism)
		self.commit = int(commit)
		self.debug = int(debug)
		self.report = int(report)
コード例 #7
0
	def __init__(self, hostname='zhoudb', dbname='graphdb', input_table='transfac.binding_site',\
		matrix_table='transfac.matrix', prom_seq_table='transfac.prom_seq', \
		output_table='graph.gene_id2mt_no', top_number=2000, acc_file=None, organism='hs', \
		commit=0, debug=0, report=0):
		self.hostname = hostname
		self.dbname = dbname
		self.input_table = input_table
		self.matrix_table = matrix_table
		self.prom_seq_table = prom_seq_table
		self.output_table = output_table
		self.top_number = int(top_number)
		self.acc_file = acc_file
		self.organism = org_short2long(organism)
		self.commit = int(commit)
		self.debug = int(debug)
		self.report = int(report)
コード例 #8
0
ファイル: prom_seq_output.py プロジェクト: polyactis/transfac
	def __init__(self, hostname='zhoudb', dbname='graphdb', schema='transfac', folder=None, \
		prefix='prom_seq_output', size=10000, organism='hs', running_type=1, debug=0, report=0, commit=0):
		"""
		2006-11-27
			add running_type
		"""
		self.hostname = hostname
		self.dbname = dbname
		self.schema = schema
		self.folder = folder
		self.prefix = prefix
		self.size = int(size)
		self.organism = org_short2long(organism)
		self.running_type = int(running_type)
		self.debug = int(debug)
		self.report = int(report)
		self.commit = int(commit)
コード例 #9
0
    def __init__(self, hostname='zhoudb', dbname='graphdb', schema='transfac', folder=None, \
     prefix='prom_seq_output', size=10000, organism='hs', running_type=1, debug=0, report=0, commit=0):
        """
		2006-11-27
			add running_type
		"""
        self.hostname = hostname
        self.dbname = dbname
        self.schema = schema
        self.folder = folder
        self.prefix = prefix
        self.size = int(size)
        self.organism = org_short2long(organism)
        self.running_type = int(running_type)
        self.debug = int(debug)
        self.report = int(report)
        self.commit = int(commit)