def geneusage_table(attr, type, outfile, g2n, n2obj, genes):
fullattr = "type2gene2%s" % attr
f = open(outfile, 'w')
f.write("Sample\t%s\n" % ("\t".join([g.lstrip("TRB") for g in genes])))
for g in sorted(g2n.keys()):
names = sorted(g2n[g])
cumul_freqs = [0.0] * len(genes)
for name in names:
gene2freq = n2obj[name][fullattr][type]
freqs = []
for i, gene in enumerate(genes):
if gene in gene2freq:
cumul_freqs[i] += gene2freq[gene]
freqs.append(gene2freq[gene])
else:
freqs.append(0.0)
pretty_freqs = [libcommon.pretty_float(freq) for freq in freqs]
f.write("%s\t%s\n" % (name, "\t".join(pretty_freqs)))
groupsize = len(names)
if groupsize > 0:
avr = [libcommon.pretty_float(freq/groupsize) for freq in cumul_freqs]
else:
avr = ['0'] * groupsize
f.write("%s_Avr\t%s\n" % (g, "\t".join(avr)))
f.close()
def table_latex_tab(f, objs, colfields):
for (name, obj) in objs:
f.write("%s" % name.replace('_', '\_'))
for attr in colfields:
if not obj or attr not in obj.getitems():
f.write(" & NA")
else:
f.write(" & %s" % libcommon.pretty_float(obj[attr]))
#f.write(" & %.3f" % obj[attr])
stdattr = "%s_std" % attr
if stdattr in obj.getitems():
std = obj[stdattr]
if std:
f.write(" $\pm$ %s" % libcommon.pretty_float(std))
f.write("\\\\\n")
f.write("\\hline\n")
def table_text_tab(f, objs, colfields):
for (name, obj) in objs:
f.write("%s" % name)
for attr in colfields:
if not obj or attr not in obj.getitems():
f.write("\tNA")
else:
f.write("\t%s" % libcommon.pretty_float(obj[attr]))
#f.write("\t%.3f" % obj[attr])
stdattr = "%s_std" % attr
if stdattr in obj.getitems():
std = obj[stdattr]
if std:
f.write(" +/- %s" % libcommon.pretty_float(std))
#f.write(" +/- %.3f" % std)
f.write("\n")
def table_latex_tab_list(f, objs, listattr):
for (name, obj) in objs:
if obj and listattr in obj.getitems():
f.write("%s & " % name.replace('_', '\_'))
vals = ["%s" % libcommon.pretty_float(v) for v in obj[listattr]]
#vals = ["%.3f" % v for v in obj[listattr]]
f.write(" & ".join(vals))
f.write("\\\\\n")
f.write("\\hline\n")
def run(self):
f = open(self.outfile, "w")
for clone, (present1, absent1, inames) in self.mjclones.iteritems():
portion1 = float(present1) / (present1 + absent1)
portion2, onames = clone_group_freq(self.c2n2s, self.names2, clone)
if portion2 <= self.opts.outgroup:
present2 = round(portion2 * len(self.names2))
absent2 = len(self.names2) - present2
tab = [[present1, present2], [absent1, absent2]]
oddratio, pval = fisher_exact(tab, alternative="greater")
if pval <= self.opts.pval:
p1 = libcommon.pretty_float(portion1)
p2 = libcommon.pretty_float(portion2)
odd = libcommon.pretty_float(oddratio)
p = libcommon.pretty_float(pval)
f.write(
"%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (clone, p1, p2, odd, p, ",".join(inames), ",".join(onames))
)
# f.write("%s\t%.2e\t%.2e\t%.2e\t%.2e\n" % (clone, present1,
# present2, oddratio, pval))
f.close()
# remove outfile if there is no significant results
if os.stat(self.outfile).st_size <= 0:
system("rm -f %s" % self.outfile)
def ttest_write(f, name, pair2tp, group2mean, pcutoff=1):
for pair, (tval, pval) in pair2tp.iteritems():
if pval <= pcutoff:
#f.write("%s\t%s\t%.2e\t%.2e" % (name, pair, tval, pval))
f.write("%s\t%s\t%s\t%s" % (name, pair,
libcommon.pretty_float(tval),
libcommon.pretty_float(pval)))
groups = pair.split("_")
(m1, std1) = group2mean[groups[0]]
(m2, std2) = group2mean[groups[1]]
#f.write("\t%.2e +/- %.2e\t%.2e +/- %.2e\n" % (m1, std1, m2, std2))
m1pretty = libcommon.pretty_float(m1)
std1pretty = libcommon.pretty_float(std1)
m2pretty = libcommon.pretty_float(m2)
std2pretty = libcommon.pretty_float(std2)
f.write("\t%s +/- %s\t%s +/- %s\n" % (m1pretty, std1pretty,
m2pretty, std2pretty))
def diversity_ttest_text(index2obj, outfile, pcutoff):
# obj: (pair2(tval, pval), group2(mean, std))
f = open(outfile, 'w')
f.write("#Index\tSample_Pair\tt_value\tp_value\tMean1\tStd1\tMean2\tStd2\n")
for index in sorted(index2obj.keys()):
obj = index2obj[index]
assert len(obj) == 2
pair2stat = obj[0]
group2mean = obj[1]
for pair in sorted(pair2stat.keys()):
tval, pval = pair2stat[pair]
if pval > pcutoff: # does not pass pcutoff
continue
groups = pair.split('_')
assert len(groups) == 2
(mean1, std1) = group2mean[groups[0]]
(mean2, std2) = group2mean[groups[1]]
vals = [tval, pval, mean1, std1, mean2, std2]
valstrs = []
for v in vals:
valstrs.append(libcommon.pretty_float(v))
f.write("%s\t%s\t%s\n" % (index, pair, '\t'.join(valstrs)))
f.close()
def table_text_tab_list(f, objs, listattr):
for (name, obj) in objs:
if obj and listattr in obj.getitems():
vals = ["%s" % libcommon.pretty_float(v) for v in obj[listattr]]
f.write("%s\t%s\n" % (name, "\t".join(vals)))