def getspecies(name, colname):
"""
Get species protein index for DB
:param name: a list contain abbreviation species nam
:param colname: a list contain colname of DB
:return: a list contain protein index can be retrieved and a match ko list (is a ko id list)
"""
dbpath = getlocaldbpath()
db = os.path.join(dbpath, "KEGG_DB_1.0.db")
relist = []
match_ko_name = []
conn = sqlite3.connect(db)
conn.text_factory = str
c = conn.cursor()
connect = "' OR NAME = '".join(name)
for ko in colname:
query = "SELECT " + ko + " FROM proindex WHERE NAME = '" + connect + "'"
c.execute(query)
ids = list(c.fetchall())
idslist = [str(x[0]) for x in ids]
if 'None' not in idslist:
relist.append(idslist)
match_ko_name.append(ko)
else:
pass
c.close()
return relist, match_ko_name
def hcp_name(index):
"""get highly conserved protein names from ko list"""
ko_path = getlocaldbpath()
pro_ko = os.path.join(ko_path, "protein_ko.txt")
with open(pro_ko) as ko:
for line in ko:
name = line.strip().split(',')
if name[1] == index:
return name[0]
def getcolname():
"""get BD colnames"""
dbpath = getlocaldbpath()
db = os.path.join(dbpath, KEGGDB)
conn = sqlite3.connect(db)
conn.text_factory = str
c = conn.cursor()
c.execute("SELECT * FROM proindex")
col_name_list = [tuple[0] for tuple in c.description]
c.close()
return col_name_list[2:]
def getspecies(spelist, colname):
"""
Get species protein index for DB
:param name: a list contain abbreviation species nam
:param colname: a list contain colname of DB
:return: a list contain protein index can be retrieved and a match ko list (is a ko id list)
"""
dbpath = getlocaldbpath()
db = os.path.join(dbpath, KEGGDB)
relist = []
match_ko_name = []
conn = sqlite3.connect(db)
conn.text_factory = str
c = conn.cursor()
if len(spelist) >= 1000:
sp = splist(spelist, 500)
else:
sp = [spelist]
for ko in colname:
tem_reslist = []
tem_none = 0
for line in sp:
connect = "' OR NAME = '".join(line)
query = "SELECT " + ko + " FROM proindex WHERE NAME = '" + connect + "'"
c.execute(query)
ids = list(c.fetchall())
idslist = [str(x[0]) for x in ids]
num_none = len([x for x in idslist if x == 'None'])
tem_none += num_none
tem_reslist.extend(idslist)
if tem_none != len(tem_reslist):
relist.append(tem_reslist)
match_ko_name.append(ko)
c.close()
return relist, match_ko_name
# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more #
# details. #
# #
# You should have received a copy of the GNU Lesser General Public License #
# along with Physpe. If not, see <http://www.gnu.org/licenses/>. #
# #
# ##############################################################################
"""
Change labels from abbreviation names to full names.
"""
from physpetool.database.dbpath import getlocaldbpath
from physpetool.utils.checkinputfile import checkFile, readIputFile
import os
dbpath = getlocaldbpath()
def taxlist():
"""
prepare Taxonomy list
:return: taxonomy list
"""
orgpath = os.path.join(dbpath, "organism.txt")
organism_list = []
with open(orgpath) as f:
for org in f:
each_org = org.strip().split('\t')
organism_list.append([each_org[1], each_org[2]])
return organism_list
# #
# ###############################################################################
"""
Check input file is right.
"""
from physpetool.database.dbpath import getlocaldbpath
from physpetool.phylotree.log import getLogging
import os
from physpetool.utils.checkIsNum import is_number
dbpath = getlocaldbpath()
logchecking = getLogging('Checking organisms')
def check_organism(input, db_list):
"""
check input organism
:param input: a list contain species name
:param db_list: a list file contain organism in corresponding database
:return: inputlist: match in database mislist: can't match in database
"""
originaList = input
inputlist = []
mislist = []
spelist = os.path.join(dbpath, db_list)
