def __call__(self, track, slice=None):
edir = EXPORTDIR
geneset = track
method = self.method
rst_text = []
for level in self.levels:
for fn in (
"%(edir)s/%(method)s/%(geneset)s_%(method)s_%(level)s_heatmap.png",
"%(edir)s/%(method)s/%(geneset)s_%(method)s_%(level)s_scvplot.png",
"%(edir)s/%(method)s/%(geneset)s_%(method)s_%(level)s_pvalue_vs_length.png"
):
f = fn % locals()
if not os.path.exists(f):
continue
rst_text.append(".. figure:: %(f)s" % locals())
if rst_text:
rst_text = '''
%(geneset)s
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
''' % locals() + "\n\n".join(rst_text)
else:
rst_text = ""
return odict((("text", rst_text), ))
def __call__(self, track, slice=None):
c = "%s_FPKM" % slice
table = track + "_levels"
if c not in self.getColumns(table):
return None
statement = '''SELECT %(slice)s_fpkm FROM %(table)s WHERE %(slice)s_fpkm > %(min_fpkm)f'''
data = self.getValues(statement)
return odict((("fpkm", data), ))
def __call__(self, track, slice=None):
vals = self.getValues("""SELECT avg(FPKM)
FROM %(track)s_cuffcompare_tracking AS t,
%(track)s_cuffcompare_transcripts AS a
WHERE code = '%(slice)s' AND
a.transfrag_id = t.transfrag_id
GROUP BY a.transfrag_id""" % locals())
return odict((("fpkm", vals), ))
def __call__(self, track, slice=None):
c = "%s_FPKM" % slice
table = track + "_levels"
if c not in self.getColumns(table):
return None
# divide by two to get relative error
statement = '''SELECT (%(slice)s_conf_hi - %(slice)s_conf_lo ) / %(slice)s_fpkm / 2
FROM %(table)s WHERE %(slice)s_fpkm > %(min_fpkm)f'''
data = self.getValues(statement)
return odict((("relative_error", data), ))
def __call__(self, track, slice=None):
c = "%s_FPKM" % slice
table = track + "_levels"
if c not in self.getColumns(table):
return None
max_fpkm = float(
self.getValue('''SELECT max(%(slice)s_fpkm) FROM %(table)s'''))
statement = '''SELECT CAST( %(slice)s_fpkm AS FLOAT) / %(max_fpkm)f FROM %(table)s WHERE %(slice)s_fpkm > %(min_fpkm)f'''
data = self.getValues(statement)
return odict((("percent of max(fpkm)", data), ))
def __call__(self, track, slice=None):
annotations = self.mAnnotations
table = self.mTable
column, where = self.mColumn, self.mWhere
if not slice or slice == "all":
data = self.getValues(
"""SELECT %(column)s FROM %(track)s_%(table)s AS d WHERE %(where)s""" % locals() )
else:
data = self.getValues( """SELECT %(column)s FROM %(track)s_%(table)s AS d, %(track)s_%(annotations)s as a
WHERE d.gene_id = a.gene_id AND a.is_%(slice)s AND %(where)s""" % locals() )
hist, bins = numpy.histogram(
data, bins=numpy.arange(0, max(data) + 1, 1))
return odict(list(zip(list(map(str, bins[:-1])), hist)))
def __call__(self, track, slice=None):
pair1, pair2 = track
a = self.get(
'''SELECT test_id, treatment_name, control_name FROM %(slice)s_%(pair1)s_gene_diff WHERE significant'''
)
b = self.get(
'''SELECT test_id, treatment_name, control_name FROM %(slice)s_%(pair2)s_gene_diff WHERE significant'''
)
a = set(map(str, a))
b = set(map(str, b))
return odict(((pair1, len(a)), (pair2, len(b)),
("shared", len(a.intersection(b)))))
def __call__(self, track, slice=None):
data = self.getFirstRow( """SELECT round(sum(length*pGC)/sum(length),3) as mean_GC,
round(sum(length*CpG_ObsExp)/sum(length),3) as mean_CpG_ObsExp,
round(sum(length*pCpG)/sum(length),3) as mean_CpG
FROM annotations.genome
WHERE id <> 'total'
AND id not like 'chrX%%'
AND id not like 'chrY%%'
AND id not like 'chrW%%'
AND id not like 'chrZ%%'
AND id not like 'chrM%%'
AND id not like '%%random%%' """ )
mColumns = ["GC content", "CpG Obs/Exp", "CpG density"]
return odict(list(zip(mColumns, data)))
def __call__(self, track, slice=None):
where = self.mWhere
select = self.mSelect
table = self.mTable
if slice == "all" or slice is None:
data = self.getFirstRow(
"%(select)s FROM %(track)s_%(table)s WHERE %(where)s" %
locals())
else:
data = self.getFirstRow(
"%(select)s FROM %(track)s_%(table)s WHERE %(where)s AND is_%slices"
% locals())
return odict(list(zip(self.mColumns, data)))
def __call__(self, track, slice=None):
data = self.getValues(
"""SELECT count(distinct gene_id) as intervals FROM (
SELECT gene_id,
CASE WHEN tss_gene_extended_pover1 > 0 THEN 'TSS'
WHEN upstream_flank_pover1 >0 THEN 'Upstream'
WHEN genes_pover1 > 0 THEN 'Gene'
WHEN downstream_flank_pover1 >0 THEN 'Downstream'
ELSE 'Intergenic'
END AS feature_class
FROM %(track)s_merged_ensembl_gene_overlap)
group by feature_class
order by feature_class asc""" % locals())
result = odict(
list(
zip(("Downstream", "Gene", "Intergenic", "TSS", "Upstream"),
data)))
return result
def __call__(self, track, slice=None):
table = self.mTable
where = self.mWhere
data = self.getValues(
""" SELECT count(distinct gene_id) as intervals FROM (
SELECT gene_id,
CASE WHEN %(where)s > 0 THEN 'TSS'
WHEN genes_pover1 > 0 THEN 'Gene'
WHEN upstream_flank_pover1 >0 THEN 'Upstream'
WHEN downstream_flank_pover1 >0 THEN 'Downstream'
ELSE 'Intergenic'
END AS feature_class
FROM %(track)s%(table)s)
group by feature_class
order by feature_class asc""" % locals())
result = odict(
list(
zip(("Downstream", "Gene", "Intergenic", "TSS", "Upstream"),
data)))
return result
def __call__(self, track, slice=None):
edir, method = EXPORTDIR, self.method
rst_text = []
geneset = track
for level in self.levels:
for x, y in itertools.combinations(EXPERIMENTS, 2):
filename = "%(edir)s/%(method)s/%(geneset)s_%(method)s_%(level)s_%(x)s_vs_%(y)s_significance.png" % locals(
)
if not os.path.exists(filename):
continue
rst_text.append('''
%(geneset)s %(level)s %(x)s vs %(y)s
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
.. figure:: %(filename)s
''' % locals())
return odict((("text", "\n".join(rst_text)), ))
def __call__(self, track, slice=None):
edir = EXPORTDIR
level = "gene"
geneset = slice
method = self.method
filename = "%(edir)s/%(method)s/%(geneset)s_%(method)s_%(level)s_fit_%(track)s.png" % locals(
)
# fitting information will not exist if there are no replicates
if not os.path.exists(filename):
return None
rst_text = '''
%(level)s %(track)s %(geneset)s
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
.. figure:: %(edir)s/%(method)s/%(geneset)s_%(method)s_%(level)s_fit_%(track)s.png
.. figure:: %(edir)s/%(method)s/%(geneset)s_%(method)s_%(level)s_residuals_%(track)s.png
''' % locals()
return odict((("text", rst_text), ))
def __call__(self, track, slice=None):
statement = '''SELECT SUM(CASE WHEN nover>0 THEN 1 ELSE 0 END) as with, SUM(CASE WHEN nover=0 THEN 1 ELSE 0 END) AS without
FROM %(track)s_merged_repeats '''
return odict(
list(zip(("with", "without"), self.getFirstRow(statement))))
def __call__(self, track, slice=None):
return odict(
(('mean',
self.getValues('''SELECT mean FROM %(track)s_mappability''')), ))
def __call__(self, track, slice=None):
statement = self.getStatement(track, slice)
if not statement:
return []
return odict(
list(zip(("with", "without"), self.getFirstRow(statement))))