本文整理汇总了Python中CGAT.Database.getTables方法的典型用法代码示例。如果您正苦于以下问题：Python Database.getTables方法的具体用法？Python Database.getTables怎么用？Python Database.getTables使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类CGAT.Database的用法示例。
在下文中一共展示了Database.getTables方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: buildExpressionStats
# 需要导入模块: from CGAT import Database [as 别名]
# 或者: from CGAT.Database import getTables [as 别名]
def buildExpressionStats(tables, method, outfile, outdir):
'''build expression summary statistics.
Creates also diagnostic plots in
<exportdir>/<method> directory.
'''
dbhandle = sqlite3.connect(PARAMS["database"])
def _split(tablename):
# this would be much easier, if feature_counts/gene_counts/etc.
# would not contain an underscore.
try:
design, geneset, counting_method = re.match(
"([^_]+)_vs_([^_]+)_(.*)_%s" % method,
tablename).groups()
except AttributeError:
try:
design, geneset = re.match(
"([^_]+)_([^_]+)_%s" % method,
tablename).groups()
counting_method = "na"
except AttributeError:
raise ValueError("can't parse tablename %s" % tablename)
return design, geneset, counting_method
# return re.match("([^_]+)_", tablename ).groups()[0]
keys_status = "OK", "NOTEST", "FAIL", "NOCALL"
outf = IOTools.openFile(outfile, "w")
outf.write("\t".join(
("design",
"geneset",
"level",
"treatment_name",
"counting_method",
"control_name",
"tested",
"\t".join(["status_%s" % x for x in keys_status]),
"significant",
"twofold")) + "\n")
all_tables = set(Database.getTables(dbhandle))
for level in CUFFDIFF_LEVELS:
for tablename in tables:
tablename_diff = "%s_%s_diff" % (tablename, level)
tablename_levels = "%s_%s_diff" % (tablename, level)
design, geneset, counting_method = _split(tablename_diff)
if tablename_diff not in all_tables:
continue
def toDict(vals, l=2):
return collections.defaultdict(
int,
[(tuple(x[:l]), x[l]) for x in vals])
tested = toDict(
Database.executewait(
dbhandle,
"SELECT treatment_name, control_name, "
"COUNT(*) FROM %(tablename_diff)s "
"GROUP BY treatment_name,control_name" % locals()
).fetchall())
status = toDict(Database.executewait(
dbhandle,
"SELECT treatment_name, control_name, status, "
"COUNT(*) FROM %(tablename_diff)s "
"GROUP BY treatment_name,control_name,status"
% locals()).fetchall(), 3)
signif = toDict(Database.executewait(
dbhandle,
"SELECT treatment_name, control_name, "
"COUNT(*) FROM %(tablename_diff)s "
"WHERE significant "
"GROUP BY treatment_name,control_name" % locals()
).fetchall())
fold2 = toDict(Database.executewait(
dbhandle,
"SELECT treatment_name, control_name, "
"COUNT(*) FROM %(tablename_diff)s "
"WHERE (l2fold >= 1 or l2fold <= -1) AND significant "
"GROUP BY treatment_name,control_name,significant"
% locals()).fetchall())
for treatment_name, control_name in tested.keys():
outf.write("\t".join(map(str, (
design,
geneset,
level,
counting_method,
treatment_name,
control_name,
tested[(treatment_name, control_name)],
"\t".join(
#.........这里部分代码省略.........
示例2: buildDMRStats
# 需要导入模块: from CGAT import Database [as 别名]
# 或者: from CGAT.Database import getTables [as 别名]
def buildDMRStats(tables, method, outfile, dbhandle):
"""build dmr summary statistics.
This method counts the number of up/down, 2fold up/down, etc.
genes in output from (:mod:`scripts/runExpression`).
This method also creates diagnostic plots in the
<exportdir>/<method> directory.
Tables should be labeled <tileset>_<design>_<method>.
Arguments
---------
tables ; list
List of tables with DMR output
method : string
Method name
outfile : string
Output filename. Tab separated file summarizing
"""
def togeneset(tablename):
return re.match("([^_]+)_", tablename).groups()[0]
keys_status = "OK", "NOTEST", "FAIL", "NOCALL"
outf = IOTools.openFile(outfile, "w")
outf.write(
"\t".join(
(
"tileset",
"design",
"track1",
"track2",
"tested",
"\t".join(["status_%s" % x for x in keys_status]),
"significant",
"up",
"down",
"twofold",
"twofold_up",
"twofold_down",
)
)
+ "\n"
)
all_tables = set(Database.getTables(dbhandle))
outdir = os.path.join(PARAMS["exportdir"], "diff_methylation")
for tablename in tables:
prefix = P.snip(tablename, "_%s" % method)
tileset, design = prefix.split("_")
def toDict(vals, l=2):
return collections.defaultdict(int, [(tuple(x[:l]), x[l]) for x in vals])
E.info("collecting data from %s" % tablename)
tested = toDict(
Database.executewait(
dbhandle,
"""SELECT treatment_name, control_name, COUNT(*)
FROM %(tablename)s
GROUP BY treatment_name,control_name"""
% locals(),
).fetchall()
)
status = toDict(
Database.executewait(
dbhandle,
"""SELECT treatment_name, control_name, status,
COUNT(*) FROM %(tablename)s
GROUP BY treatment_name,control_name,status"""
% locals(),
).fetchall(),
3,
)
signif = toDict(
Database.executewait(
dbhandle,
"""SELECT treatment_name, control_name,
COUNT(*) FROM %(tablename)s
WHERE significant
GROUP BY treatment_name,control_name"""
% locals(),
).fetchall()
)
fold2 = toDict(
Database.executewait(
dbhandle,
"""SELECT treatment_name, control_name,
COUNT(*) FROM %(tablename)s
WHERE (l2fold >= 1 or l2fold <= -1) AND significant
GROUP BY treatment_name,control_name,significant"""
% locals(),
).fetchall()
)
#.........这里部分代码省略.........