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")
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)
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)
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)
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)
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)
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)
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)
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)