def test_allkinds(self):
format = 'pdf'
from bbcflib.gfminer.figure import venn
D1 = {'A':126}
D2 = {'Albert':126, 'Barthur':247, 'Albert|Barthur':50}
D31 = {'Ar':521, 'Bi':14, 'Co':290, 'Ar|Bi':11, 'Ar|Co':100, 'Bi|Co':4, 'Ar|Bi|Co':1}
D32 = {'A':521, 'B':300, 'C':290, 'A|B':11, 'A|C':100, 'B|C':44, 'A|B|C':5}
D4 = {'A':210, 'B':220, 'C':230, 'D':240,
'A|B':80, 'A|C':80, 'A|D':80, 'B|C':80, 'B|D':80, 'C|D':80,
'A|B|C':30, 'A|B|D':30, 'A|C|D':30, 'B|C|D':30, 'A|B|C|D':10}
venn(D1,output=path+'d1.'+format,legend=['file1.bed'],format=format)
venn(D2,output=path+'d2.'+format,format=format)
venn(D31,output=path+'d3.1.'+format,format=format)
venn(D32,output=path+'d3.2.'+format,legend=['file1','file2','file3'],format=format)
venn(D4,output=path+'d4.'+format,legend=['file1','file2','file3','file4'],format=format)
def __call__(self,**kw):
files_list = kw['SigMulti']['files']
column = int(kw['column'])-1
output = self.temporary_path(fname='intersections.')
counts,legend = self.compare(files_list, output, column)
# compress
output_targz = self.temporary_path(fname=output+'tar.gz')
tar = tarfile.open(output_targz, 'w:gz')
tar.add(output)
tar.close()
self.new_file(output+'.tar.gz', 'intersections')
if len(files_list) <= 4:
# Venn diagram
venn_format = 'png'
venn_outname = self.temporary_path(fname='venn'+venn_format)
venn(counts,legend=None,options={},output=venn_outname,format=venn_format)
self.new_file(venn_outname, 'venn_diagram')
return self.display_time()
def __call__(self, **kw):
files_list = kw['SigMulti']['files']
column = int(kw['column']) - 1
output = self.temporary_path(fname='intersections.')
counts, legend = self.compare(files_list, output, column)
# compress
output_targz = self.temporary_path(fname=output + 'tar.gz')
tar = tarfile.open(output_targz, 'w:gz')
tar.add(output)
tar.close()
self.new_file(output + '.tar.gz', 'intersections')
if len(files_list) <= 4:
# Venn diagram
venn_format = 'png'
venn_outname = self.temporary_path(fname='venn' + venn_format)
venn(counts,
legend=None,
options={},
output=venn_outname,
format=venn_format)
self.new_file(venn_outname, 'venn_diagram')
return self.display_time()
def __call__(self, **kw):
def _parse_logic(string):
s = re.sub(r'[^\w\d!=><\. ]', '', string)
s = re.sub(r' OR ', ')or(%f ', s)
s = re.sub(r' AND ', ')and(%f ', s)
return "(%f "+s+")"
def _run_test(row, indx, cond):
num = float(row[col_ind[indx]])
num = max(-sys.maxint,min(sys.maxint,num))
num = (num,)*c.count("%f")
return eval(cond % (num))
def _add_label(s,x):
_f = s.fields+['track_name']
return FeatureStream((y+(x,) for y in s), fields=_f)
venn_options = {} # tune it here
tracks = []
intype = kw.get("input_type") or "Table"
if intype == "Table":
s_cols = kw.get('id_columns','')
s_filters = kw.get('filters','')
infile = track(kw.get('table',''),format='txt',header=True)
col_ind = [int(i)-1 for i in s_cols.split(",")]
legend = [infile.fields[i] if i<len(infile.fields) else str(i) for i in col_ind]
conds = [_parse_logic(x) for x in s_filters.split(",")]
tlabels = [chr(k+65) for k in range(len(col_ind))]
conds += ["1"]*(len(col_ind)-len(conds))
combn = [tuple(sorted(x)) for k in range(len(tlabels))
for x in combinations(tlabels,k+1)]
c1 = dict(("|".join(c),0) for c in combn)
c2 = dict(("|".join(c),0) for c in combn)
indx = dict((c,[tlabels.index(x) for x in c]) for c in combn)
for row in infile:
tests = [_run_test(row,i,c) for i,c in enumerate(conds)]
for c in combn:
c1["|".join([tlabels[n] for n,t in enumerate(tests) if t])] += 1
c2["|".join(c)] += all([tests[i] for i in indx[c]])
nsamples = len(col_ind)
combn = ['|'.join(y) for x in combn for y in x]
elif intype == "Tracks":
#filenames = kw['TrMulti']['files']
filenames = kw['files']
if not isinstance(filenames,(list,tuple)): filenames = [filenames]
for f in filenames: assert os.path.exists(f), "File not found: %s ." % f
tracks = [track(f,chrmeta='guess') for f in filenames]
nsamples = len(tracks)
tlabels = [chr(k+65) for k in range(len(tracks))]
combn = [combinations(tlabels,k+1) for k in range(len(tlabels))]
combn = ['|'.join(sorted(y)) for x in combn for y in x]
c1 = dict(zip(combn,[0]*len(combn)))
c2 = dict(zip(combn,[0]*len(combn)))
total_cov = 0.0
_scored = (kw.get('type') == 'score')
chromset = set([c for t in tracks for c in t.chrmeta])
for chrom in chromset:
streams = [_add_label(t.read(chrom),tlabels[n]) for n,t in enumerate(tracks)]
s = cobble(concatenate(streams),scored=_scored)
name_idx = s.fields.index('track_name')
start_idx = s.fields.index('start')
end_idx = s.fields.index('end')
if _scored: score_idx = s.fields.index('score')
for x in s:
length = x[end_idx]-x[start_idx]
total_cov += length
sub = sorted(list(set(x[name_idx].split('|')))) # avoid 'A|A'
cb = [combinations(sub,k) for k in range(1,len(sub)+1)]
cb = ['|'.join(sorted(y)) for c in cb for y in c]
if _scored:
c1['|'.join(sub)] += x[score_idx]
for c in cb: c2[c] += x[score_idx]
else:
c1['|'.join(sub)] += length
for c in cb: c2[c] += length
if total_cov < 1:
output = self.temporary_path(fname='venn_summary.txt')
with open(output,'wb') as summary:
summary.write("Empty content (no coverage) on %s." %(",".join(chromset)))
self.new_file(output, 'venn_summary')
return
legend = [t.name for t in tracks]
if _scored:
for c in combn:
c2[c] = round(c2[c])
else:
for c in combn:
c2[c] = round((100*c2[c])/total_cov)
c1[c] = (100*c1[c])/total_cov
else:
raise ValueError("Input type '%s' not supported." %intype)
if nsamples <= 4:
format = kw.get('output') or 'pdf'
output = self.temporary_path(fname='venn_diagram.'+format)
venn(c2,legend=legend,options=venn_options,output=output,format=format)
self.new_file(output, 'venn_diagram')
# Text summary
output = self.temporary_path(fname='venn_summary.txt')
with open(output,'w') as summary:
summary.write("%s\t%s\t%s\n" % ("Group","Coverage", "Cumulative coverage"))
record = "%s\t%.2f\t%d\n"
for c in sorted(combn, key=lambda x:(len(x),x)):
summary.write(record%(c,c1[c],c2[c]))
self.new_file(output, 'venn_summary')
return self.display_time()
def __call__(self, **kw):
def _parse_logic(string):
s = re.sub(r'[^\w\d!=><\. ]', '', string)
s = re.sub(r' OR ', ')or(%f ', s)
s = re.sub(r' AND ', ')and(%f ', s)
return "(%f " + s + ")"
def _run_test(row, indx, cond):
num = float(row[col_ind[indx]])
num = max(-sys.maxint, min(sys.maxint, num))
num = (num, ) * c.count("%f")
return eval(cond % (num))
def _add_label(s, x):
_f = s.fields + ['track_name']
return FeatureStream((y + (x, ) for y in s), fields=_f)
venn_options = {} # tune it here
tracks = []
intype = kw.get("input_type") or "Table"
if intype == "Table":
s_cols = kw.get('id_columns', '')
s_filters = kw.get('filters', '')
infile = track(kw.get('table', ''), format='txt', header=True)
col_ind = [int(i) - 1 for i in s_cols.split(",")]
legend = [
infile.fields[i] if i < len(infile.fields) else str(i)
for i in col_ind
]
conds = [_parse_logic(x) for x in s_filters.split(",")]
tlabels = [chr(k + 65) for k in range(len(col_ind))]
conds += ["1"] * (len(col_ind) - len(conds))
combn = [
tuple(sorted(x)) for k in range(len(tlabels))
for x in combinations(tlabels, k + 1)
]
c1 = dict(("|".join(c), 0) for c in combn)
c2 = dict(("|".join(c), 0) for c in combn)
indx = dict((c, [tlabels.index(x) for x in c]) for c in combn)
for row in infile:
tests = [_run_test(row, i, c) for i, c in enumerate(conds)]
for c in combn:
c1["|".join([tlabels[n] for n, t in enumerate(tests)
if t])] += 1
c2["|".join(c)] += all([tests[i] for i in indx[c]])
nsamples = len(col_ind)
combn = ['|'.join(y) for x in combn for y in x]
elif intype == "Tracks":
filenames = kw['TrMulti']['files']
if not isinstance(filenames, (list, tuple)):
filenames = [filenames]
for f in filenames:
assert os.path.exists(f), "File not found: %s ." % f
tracks = [track(f, chrmeta='guess') for f in filenames]
nsamples = len(tracks)
tlabels = [chr(k + 65) for k in range(len(tracks))]
combn = [combinations(tlabels, k + 1) for k in range(len(tlabels))]
combn = ['|'.join(sorted(y)) for x in combn for y in x]
c1 = dict(zip(combn, [0] * len(combn)))
c2 = dict(zip(combn, [0] * len(combn)))
total_cov = 0.0
_scored = (kw.get('type') == 'score')
chromset = set([c for t in tracks for c in t.chrmeta])
for chrom in chromset:
streams = [
_add_label(t.read(chrom), tlabels[n])
for n, t in enumerate(tracks)
]
s = cobble(concatenate(streams), scored=_scored)
name_idx = s.fields.index('track_name')
start_idx = s.fields.index('start')
end_idx = s.fields.index('end')
if _scored: score_idx = s.fields.index('score')
for x in s:
length = x[end_idx] - x[start_idx]
total_cov += length
sub = sorted(list(set(
x[name_idx].split('|')))) # avoid 'A|A'
cb = [combinations(sub, k) for k in range(1, len(sub) + 1)]
cb = ['|'.join(sorted(y)) for c in cb for y in c]
if _scored:
c1['|'.join(sub)] += x[score_idx]
for c in cb:
c2[c] += x[score_idx]
else:
c1['|'.join(sub)] += length
for c in cb:
c2[c] += length
if total_cov < 1:
output = self.temporary_path(fname='venn_summary.txt')
with open(output, 'wb') as summary:
summary.write("Empty content (no coverage) on %s." %
(",".join(chromset)))
self.new_file(output, 'venn_summary')
return
legend = [t.name for t in tracks]
if _scored:
for c in combn:
c2[c] = round(c2[c])
else:
for c in combn:
c2[c] = round((100 * c2[c]) / total_cov)
c1[c] = (100 * c1[c]) / total_cov
else:
raise ValueError("Input type '%s' not supported." % intype)
if nsamples <= 4:
format = kw.get('format') or 'pdf'
output = self.temporary_path(fname='venn_diagram.' + format)
venn(c2,
legend=legend,
options=venn_options,
output=output,
format=format)
self.new_file(output, 'venn_diagram')
# Text summary
output = self.temporary_path(fname='venn_summary.txt')
with open(output, 'w') as summary:
summary.write("%s\t%s\t%s\n" %
("Group", "Coverage", "Cumulative coverage"))
record = "%s\t%.2f\t%d\n"
for c in sorted(combn, key=lambda x: (len(x), x)):
summary.write(record % (c, c1[c], c2[c]))
self.new_file(output, 'venn_summary')
return self.display_time()