def tab(f, rowname2cells, index2colname):
for rowname in sorted( rowname2cells.keys() ):
row = rowname2cells[rowname]
f.write("%s" %rowname)
for i, m in enumerate( row ):
if i % 2 == 0 and m != 'NA' and m != '' and m != '-':
colname = index2colname[i]
if colname in ['uniqClones', 'fisherAlpha']:
f.write( " & %s " % iseqlib.prettyInt( int(float(m)) ) )
else:
f.write( " & %.3f " % float(m) )
elif i%2 == 1 and m != 'NA' and m != '' and m != '-':
colname = index2colname[i -1]
if colname in ['uniqClones', 'fisherAlpha']:
f.write( " $\\pm$ %s " % iseqlib.prettyInt(int(float(m))) )
else:
f.write( " $\\pm$ %.3f " % float(m) )
f.write("\\\\\n")
f.write("\\hline\n")
def getClonesizeTextTab(samples, groupsamples, group2samples, outfile, simpson):
if len(groupsamples) >0:
samples = sortSamplesByGroup(samples, groupsamples, group2samples)
else:
samples = sorted(samples, key=lambda sample: sample.totalCount)
f = open(outfile, 'w')
if simpson:
f.write("Sample\tClones\tTotal Reads\tSimpson Index\n")
else:
f.write("Sample\tClones\tTotal Reads\n")
for s in samples:
if s.name in group2samples:
f.write("Avr %s\t%s\t%s" %(s.name.replace('_', "-"), iseqlib.prettyInt(s.totalClones), iseqlib.prettyInt(s.totalCount)))
if simpson:
f.write("\t%.3f" %s.simpson)
f.write("\n")
f.write("#\n")
else:
f.write("%s\t%s\t%s" %(s.name.replace('_', "-"), iseqlib.prettyInt(s.totalClones), iseqlib.prettyInt(s.totalCount)))
if simpson:
f.write("\t%.3f" %s.simpson)
f.write("\n")
f.close()
def tab(f, samples, groupsamples, group2samples, simpson):
if len(groupsamples) > 0:
samples = sortSamplesByGroup(samples, groupsamples, group2samples)
for s in samples:
if s.name in group2samples:
f.write("\\cellcolor[gray]{0.9} Avr %s & \\cellcolor[gray]{0.9} %s & \\cellcolor[gray]{0.9} %s" %(s.name.replace('_', "-"), iseqlib.prettyInt(s.totalClones), iseqlib.prettyInt(s.totalCount)))
if simpson:
f.write("& \\cellcolor[gray]{0.9} %.3f" % s.simpson)
f.write("\\\\\n")
f.write("\\hline\n")
else:
f.write("%s & %s & %s" %(s.name.replace('_', "-"), iseqlib.prettyInt(s.totalClones), iseqlib.prettyInt(s.totalCount)))
if simpson:
f.write("& %.3f" %s.simpson)
f.write("\\\\\n")
if len(groupsamples) == 0:
f.write("\\hline\n")
def textTab(f, sampleToExps, cutoff, sampleOrder):
#f.write("#S1\tS2\tSize\tClones1\tClones2\t%O.Clones1\t%O.Clones2\t%O.Reads1\t%O.Reads2\n")
f.write("#S1\tS2\tSize\tClones1\t%O.Clones1\t%O.Reads1\tClones2\t%O.Clones2\t%O.Reads2\n")
samples = sampleOrder
if not sampleOrder:
samples = sorted( sampleToExps.keys() )
for sample in samples:
exps = sampleToExps[sample]
for exp in exps:
#Find index of the cutoff
index = -1
for i,c in enumerate(exp.cutoffs):
if c == cutoff:
index = i
break
if index == -1:
continue
samsize = str(exp.size)
if samsize == '0':
samsize = 'NA'
if exp.sample1 == sample:
f.write("%s\t%s\t%s\t%s\t%.2f\t%.2f\t%s\t%.2f\t%.2f \n" %(exp.sample1, exp.sample2, samsize, iseqlib.prettyInt(int(exp.clones1[index])), exp.oclones1[index], exp.reads1o2[index], iseqlib.prettyInt(int(exp.clones2[index])), exp.oclones2[index], exp.reads2o1[index]) )
#f.write("%s\t%s\t%s\t%s\t%s\t%.2f\t%.2f\t%.2f\t%.2f \n" %(exp.sample1, exp.sample2, samsize, iseqlib.prettyInt(int(exp.clones1[index])), iseqlib.prettyInt(int(exp.clones2[index])), exp.oclones1[index], exp.oclones2[index], exp.reads1o2[index], exp.reads2o1[index]) )
else:
f.write("%s\t%s\t%s\t%s\t%.2f\t%.2f\t%s\t%.2f\t%.2f \n" %(exp.sample2, exp.sample1, samsize, iseqlib.prettyInt(int(exp.clones2[index])), exp.oclones2[index], exp.reads2o1[index], iseqlib.prettyInt(int(exp.clones1[index])), exp.oclones1[index], exp.reads1o2[index]) )
#f.write("%s\t%s\t%s\t%s\t%s\t%.2f\t%.2f\t%.2f\t%.2f \n" %(exp.sample2, exp.sample1, samsize, iseqlib.prettyInt(int(exp.clones2[index])), iseqlib.prettyInt(int(exp.clones1[index])), exp.oclones2[index], exp.oclones1[index], exp.reads2o1[index], exp.reads1o2[index]) )
f.write("#\n")
def tab2(f, sampleToExps, cutoff, sampleOrder):
samples = sampleOrder
if not sampleOrder:
samples = sorted( sampleToExps.keys() )
for sample in samples:
exps = sampleToExps[sample]
for exp in exps:
#Find index of the cutoff
index = -1
for i,c in enumerate(exp.cutoffs):
if c == cutoff:
index = i
break
if index == -1:
continue
samsize = str(exp.size)
if samsize == '0':
samsize = 'NA'
if exp.sample1 == sample:
#f.write("%s & %s & %s & %s & %s & %.2f & %.2f & %.2f & %.2f \\\\\n" %(exp.sample1, exp.sample2, samsize, iseqlib.prettyInt(int(exp.clones1[index])), iseqlib.prettyInt(int(exp.clones2[index])), exp.oclones1[index], exp.oclones2[index], exp.reads1o2[index], exp.reads2o1[index]) )
f.write("%s & %s & %s & %s & %.2f & %.2f & %s & %.2f & %.2f \\\\\n" %(exp.sample1, exp.sample2, samsize, iseqlib.prettyInt(int(exp.clones1[index])), exp.oclones1[index], exp.reads1o2[index], iseqlib.prettyInt(int(exp.clones2[index])), exp.oclones2[index], exp.reads2o1[index]) )
else:
#f.write("%s & %s & %s & %s & %s & %.2f & %.2f & %.2f & %.2f \\\\\n" %(exp.sample2, exp.sample1, samsize, iseqlib.prettyInt(int(exp.clones2[index])), iseqlib.prettyInt(int(exp.clones1[index])), exp.oclones2[index], exp.oclones1[index], exp.reads2o1[index], exp.reads1o2[index]) )
f.write("%s & %s & %s & %s & %.2f & %.2f & %s & %.2f & %.2f \\\\\n" %(exp.sample2, exp.sample1, samsize, iseqlib.prettyInt(int(exp.clones2[index])), exp.oclones2[index], exp.reads2o1[index], iseqlib.prettyInt(int(exp.clones1[index])), exp.oclones1[index], exp.reads1o2[index]) )
f.write("\\hline\n")