def libs(args):
"""
%prog libs libfile
Get list of lib_ids to be run by pull(). The SQL commands:
select library.lib_id, library.name from library join bac on
library.bac_id=bac.id where bac.lib_name="Medicago";
select seq_name from sequence where seq_name like 'MBE%'
and trash is null;
"""
p = OptionParser(libs.__doc__)
p.set_db_opts(dbname="track", credentials=None)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
libfile, = args
sqlcmd = "select library.lib_id, library.name, bac.gb# from library join bac on " + \
"library.bac_id=bac.id where bac.lib_name='Medicago'"
cur = connect(opts.dbname)
results = fetchall(cur, sqlcmd)
fw = open(libfile, "w")
for lib_id, name, gb in results:
name = name.translate(None, "\n")
if not gb:
gb = "None"
print >> fw, "|".join((lib_id, name, gb))
fw.close()
def libs(args):
"""
%prog libs libfile
Get list of lib_ids to be run by pull(). The SQL commands:
select library.lib_id, library.name from library join bac on
library.bac_id=bac.id where bac.lib_name="Medicago";
select seq_name from sequence where seq_name like 'MBE%'
and trash is null;
"""
p = OptionParser(libs.__doc__)
p.set_db_opts(dbname="track", credentials=None)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
libfile, = args
sqlcmd = "select library.lib_id, library.name, bac.gb# from library join bac on " + \
"library.bac_id=bac.id where bac.lib_name='Medicago'"
cur = connect(opts.dbname)
results = fetchall(cur, sqlcmd)
fw = open(libfile, "w")
for lib_id, name, gb in results:
name = name.translate(None, "\n")
if not gb:
gb = "None"
print >> fw, "|".join((lib_id, name, gb))
fw.close()
def pull(args):
"""
%prog pull libfile
Pull the sequences using the first column in the libfile.
"""
p = OptionParser(pull.__doc__)
p.set_db_opts(dbname="mtg2", credentials=None)
p.add_option(
"--frag",
default=False,
action="store_true",
help="The command to pull sequences from db",
)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(libfile, ) = args
dbname = opts.dbname
frag = opts.frag
fp = open(libfile)
hostname, username, password = get_profile()
for row in fp:
lib_id, name = row.split("|", 1)
sqlfile = lib_id + ".sql"
if not op.exists(sqlfile):
fw = open(sqlfile, "w")
print(
"select seq_name from sequence where seq_name like" +
" '{0}%' and trash is null".format(lib_id),
file=fw,
)
fw.close()
if frag:
cmd = "pullfrag -D {0} -n {1}.sql -o {1} -q -S {2}".format(
dbname, lib_id, hostname)
cmd += " -U {0} -P {1}".format(username, password)
else:
cmd = "pullseq -D {0} -n {1}.sql -o {1} -q".format(dbname, lib_id)
sh(cmd)
def pull(args):
"""
%prog pull libfile
Pull the sequences using the first column in the libfile.
"""
p = OptionParser(pull.__doc__)
p.set_db_opts(dbname="mtg2", credentials=None)
p.add_option(
"--frag", default=False, action="store_true", help="The command to pull sequences from db [default: %default]"
)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
libfile, = args
dbname = opts.dbname
frag = opts.frag
fp = open(libfile)
hostname, username, password = get_profile()
for row in fp:
lib_id, name = row.split("|", 1)
sqlfile = lib_id + ".sql"
if not op.exists(sqlfile):
fw = open(sqlfile, "w")
print >> fw, "select seq_name from sequence where seq_name like" + " '{0}%' and trash is null".format(
lib_id
)
fw.close()
if frag:
cmd = "pullfrag -D {0} -n {1}.sql -o {1} -q -S {2}".format(dbname, lib_id, hostname)
cmd += " -U {0} -P {1}".format(username, password)
else:
cmd = "pullseq -D {0} -n {1}.sql -o {1} -q".format(dbname, lib_id)
sh(cmd)
def query(args):
"""
%prog query "SELECT feat_name FROM asm_feature WHERE feat_type = \\"{0}\\" AND end5 <= \\"{1}\\" AND end3 >= \\"{2}\\"" ::: datafile1 ....
Script takes the data from tab-delimited datafile(s) and replaces the placeholders
in the query which is then executed. Depending upon the type of query, results are
either printed out (when running `select`) or not (when running `insert`, `update`
or `delete`)
If the query contains quotes around field values, then these need to be escaped with \\
"""
p = OptionParser(query.__doc__)
p.set_db_opts()
p.add_option(
"--dryrun",
default=False,
action="store_true",
help="Don't commit to database. Just print queries [default: %default]"
)
p.set_sep(help="Specify output field separator")
p.set_verbose(help="Print out all the queries")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) == 0:
sys.exit(not p.print_help())
fieldsep = opts.sep
sep = ":::"
files = None
if sep in args:
sepidx = args.index(sep)
files = args[sepidx + 1:]
args = args[:sepidx]
if not files:
files = [""]
qrys = []
qry = " ".join(args)
if ";" in qry:
for q in qry.split(";"):
if len(q.strip()) > 0:
qrys.append(q)
else:
qrys.append(qry)
queries = set()
if files:
for datafile in files:
datafile = datafile.strip()
fp = must_open(datafile)
for row in fp:
for qry in qrys:
qry = qry.strip()
m = re.findall(r"\{\d+\}", qry)
if m:
mi = [int(x.strip("{}")) for x in m]
atoms = row.strip().split("\t")
assert max(mi) <= len(atoms), \
"Number of columns in `datafile`({0})".format(len(atoms)) + \
" != number of `placeholders`({0})".format(len(m))
natoms = [atoms[x] for x in mi]
for idx, (match, atom) in enumerate(zip(m, natoms)):
qry = qry.replace(match, atom)
queries.add(qry)
else:
for qry in qrys:
if re.search(r"\{\d+\}", qry):
logging.error(
"Query `{0}` contains placeholders, no datafile(s) specified"
.format(qry))
sys.exit()
queries.add(qry)
if not opts.dryrun:
fw = must_open(opts.outfile, "w")
dbh, cur = connect(opts.dbname, connector=opts.dbconn, hostname=opts.hostname, \
username=opts.username, password=opts.password, port=opts.port)
cflag = None
for qry in queries:
if opts.dryrun or opts.verbose:
print qry
if not opts.dryrun:
if to_commit(qry):
execute(cur, qry)
cflag = True
else:
results = fetchall(cur, qry, connector=opts.dbconn)
for result in results:
print >> fw, fieldsep.join([str(x) for x in result])
if not opts.dryrun and cflag:
commit(dbh)
def query(args):
"""
%prog query "SELECT feat_name FROM asm_feature WHERE feat_type = \\"{0}\\" AND end5 <= \\"{1}\\" AND end3 >= \\"{2}\\"" ::: datafile1 ....
Script takes the data from tab-delimited datafile(s) and replaces the placeholders
in the query which is then executed. Depending upon the type of query, results are
either printed out (when running `select`) or not (when running `insert`, `update`
or `delete`)
If the query contains quotes around field values, then these need to be escaped with \\
"""
p = OptionParser(query.__doc__)
p.set_db_opts()
p.add_option("--dryrun", default=False, action="store_true",
help="Don't commit to database. Just print queries [default: %default]")
p.set_sep(help="Specify output field separator")
p.set_verbose(help="Print out all the queries")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) == 0:
sys.exit(not p.print_help())
fieldsep = opts.sep
sep = ":::"
files = None
if sep in args:
sepidx = args.index(sep)
files = args[sepidx + 1:]
args = args[:sepidx]
if not files:
files = [""]
qrys = []
qry = " ".join(args)
if ";" in qry:
for q in qry.split(";"):
if len(q.strip()) > 0:
qrys.append(q)
else:
qrys.append(qry)
queries = set()
if files:
for datafile in files:
datafile = datafile.strip()
fp = must_open(datafile)
for row in fp:
for qry in qrys:
qry = qry.strip()
m = re.findall(r"\{\d+\}", qry)
if m:
mi = [int(x.strip("{}")) for x in m]
atoms = row.strip().split("\t")
assert max(mi) <= len(atoms), \
"Number of columns in `datafile`({0})".format(len(atoms)) + \
" != number of `placeholders`({0})".format(len(m))
natoms = [atoms[x] for x in mi]
for idx, (match, atom) in enumerate(zip(m, natoms)):
qry = qry.replace(match, atom)
queries.add(qry)
else:
for qry in qrys:
if re.search(r"\{\d+\}", qry):
logging.error("Query `{0}` contains placeholders, no datafile(s) specified".format(qry))
sys.exit()
queries.add(qry)
if not opts.dryrun:
fw = must_open(opts.outfile, "w")
dbh, cur = connect(opts.dbname, connector=opts.dbconn, hostname=opts.hostname, \
username=opts.username, password=opts.password, port=opts.port)
cflag = None
for qry in queries:
if opts.dryrun or opts.verbose:
print qry
if not opts.dryrun:
if to_commit(qry):
execute(cur, qry)
cflag = True
else:
results = fetchall(cur, qry)
for result in results:
print >> fw, fieldsep.join([str(x) for x in result])
if not opts.dryrun and cflag:
commit(dbh)