def getWtssDBConnection(db=''):
"""Get access to the database specified in the config file."""
wtss_param = utils_param.get_wtss_parameter()
mysql_dbh = getDbConnection(db, wtss_param.get_mysql_user(),
wtss_param.get_mysql_password(),
wtss_param.get_mysql_host())
return mysql_dbh
def getWtssDBConnection(db=''):
"""Get access to the database specified in the config file."""
wtss_param=utils_param.get_wtss_parameter()
mysql_dbh=getDbConnection(db, wtss_param.get_mysql_user(),
wtss_param.get_mysql_password(),
wtss_param.get_mysql_host())
return mysql_dbh
def get_list_contig_file(sp_code,wtss_param=None):
if not wtss_param:
wtss_param=utils_param.get_wtss_parameter()
list_contig_file=wtss_param.get_list_contig_file(sp_code)
if not list_contig_file:
samtools_bin=os.path.join(wtss_param.get_samtools_dir(),'samtools')
genome_fasta=wtss_param.get_genome_fasta(sp_code)
list_contig_file=generate_fai_from_genome(genome_fasta=genome_fasta, samtools_bin=samtools_bin)
if not list_contig_file:
logging.error("Can't create the .fai file from the genome fasta using %s on %s"%(samtools_bin,genome_fasta))
return list_contig_file
def get_list_contig_file(sp_code, wtss_param=None):
if not wtss_param:
wtss_param = utils_param.get_wtss_parameter()
list_contig_file = wtss_param.get_list_contig_file(sp_code)
if not list_contig_file:
samtools_bin = os.path.join(wtss_param.get_samtools_dir(), 'samtools')
genome_fasta = wtss_param.get_genome_fasta(sp_code)
list_contig_file = generate_fai_from_genome(genome_fasta=genome_fasta,
samtools_bin=samtools_bin)
if not list_contig_file:
logging.error(
"Can't create the .fai file from the genome fasta using %s on %s"
% (samtools_bin, genome_fasta))
return list_contig_file
def get_sp_code(specie, available_species=None):
if specie:
sp_lo=specie.lower()
if not available_species:
wtss_param=utils_param.get_wtss_parameter()
available_species=wtss_param.get_available_species()
if not available_species:
#keep for backward compatibility
available_species={'hs':['human','homo_sapiens','hs', '9606'],
'mm':['mouse', 'mus_musculus', 'mm', '10090'],
'pt':['poplar', 'populus_trichocarpa', 'pt', '3694'],
'ce':['worm', 'c_elegans', 'ce', '6239']}
for sp in available_species.keys():
if sp_lo in available_species.get(sp) or specie in available_species.get(sp):
return sp
return None
def get_sp_code(specie, available_species=None):
if specie:
sp_lo = specie.lower()
if not available_species:
wtss_param = utils_param.get_wtss_parameter()
available_species = wtss_param.get_available_species()
if not available_species:
#keep for backward compatibility
available_species = {
'hs': ['human', 'homo_sapiens', 'hs', '9606'],
'mm': ['mouse', 'mus_musculus', 'mm', '10090'],
'pt': ['poplar', 'populus_trichocarpa', 'pt', '3694'],
'ce': ['worm', 'c_elegans', 'ce', '6239']
}
for sp in available_species.keys():
if sp_lo in available_species.get(
sp) or specie in available_species.get(sp):
return sp
return None
