def tab(f, stats, sample2repeat):
altColor = 1
for sample in stats:
repeat = 'NA'
repeatPc = ''
if sample.name in sample2repeat:
repeat = libplot.prettyInt( sample2repeat[sample.name][1] )
repeatPc = "(%.2f \\%%)" %sample2repeat[sample.name][2]
otherRef = libplot.prettyInt(sample.otherReferenceBasesMapped)
otherRefPc = "%.2f" % (100.0*sample.otherReferenceBasesMapped/sample.totalBases)
ref = libplot.prettyInt(sample.referenceBasesMapped)
refPc = "%.2f" % (100.0*sample.referenceBasesMapped/sample.totalBases)
total = libplot.prettyInt(sample.totalBases)
sampleName = libplot.properName(sample.name)
if altColor == 1:
f.write("%s & %s %s & %s (%s \\%%) & %s (%s \\%%) & %s \\\\\n" %(sampleName, repeat, repeatPc, otherRef, otherRefPc, ref, refPc, total ))
else:
f.write("\\cellcolor[gray]{0.9} %s & \\cellcolor[gray]{0.9} %s %s & \\cellcolor[gray]{0.9} %s (%s \\%%) & \\cellcolor[gray]{0.9} %s (%s \\%%) & \\cellcolor[gray]{0.9} %s \\\\\n" %(sampleName, repeat, repeatPc, otherRef, otherRefPc, ref, refPc, total ))
altColor = 1 - altColor
f.write("\\hline\n")
def tab( f, exps, rexps, samples ):
for sample in samples:
expList = copy.copy(exps[sample])
expList.sort()
expList.append( rexps[sample] )
#sys.stderr.write('expList for sample %s: %s\n' %(sample, '\t'.join([ '%s%d' %(e.ref, e.weight)for e in expList])))
f.write( "\\multirow{%d}{*}{%s} " %( len(expList), sample ) )
#f.write( "\\multirow{%d}{*}{%s} " %( len(expList) -1, sample ) ) #HACK
for e in expList:
#if e.ref == 'cactusRef' and e.weight == 1: #HACK
# continue
ref = libplot.properName(e.ref)
if re.search('cactusRef', e.ref):
r = e.ref.lstrip('cactusRef')
ref = "%s %s" % (libplot.properName('cactusRef'), r)
if e.ref != 'cactusRef':
f.write("& %s & %s & %s & %s & %s & %s \\\\\n" %(ref, libplot.prettyInt(e.mapped), libplot.prettyInt(e.uniquelyMapped), libplot.prettyInt(e.properlyPaired), libplot.prettyInt(e.uniquelyMappedAndProperlyPaired), libplot.prettyInt(e.snps)))
elif e.ref == 'cactusRef' and e.weight == 2:
f.write("& \\cellcolor{cyan!30} %s%d & \\cellcolor{cyan!30} %s & \\cellcolor{cyan!30} %s & \\cellcolor{cyan!30} %s & \\cellcolor{cyan!30} %s & \\cellcolor{cyan!30} %s \\\\\n" %(ref, e.weight, libplot.prettyInt(e.mapped), libplot.prettyInt(e.uniquelyMapped), libplot.prettyInt(e.properlyPaired), libplot.prettyInt(e.uniquelyMappedAndProperlyPaired), libplot.prettyInt(e.snps)))
else:
f.write("& %s%d & %s & %s & %s & %s & %s \\\\\n" %(ref, e.weight, libplot.prettyInt(e.mapped), libplot.prettyInt(e.uniquelyMapped), libplot.prettyInt(e.properlyPaired), libplot.prettyInt(e.uniquelyMappedAndProperlyPaired), libplot.prettyInt(e.snps)))
f.write("\\hline\n")
def tab(f, data ):
altColor = 1
sortedsamples = sorted( data.keys() )
for i,s in enumerate(sortedsamples):
if s == 'average':
sortedsamples.pop(i)
sortedsamples.append('average')
for sample in sorted( data.keys() ):
stats = data[sample]
if altColor == 1:
f.write( "%s & %s & %s & %.2f \\%% & %.4f & %.4f\\\\\n" %(sample, libplot.prettyInt(stats[0]), libplot.prettyInt(stats[1]), stats[2], stats[3], stats[3]/stats[4]) )
else:
f.write( "\\cellcolor[gray]{0.9} %s & \\cellcolor[gray]{0.9} %s & \\cellcolor[gray]{0.9} %s & \\cellcolor[gray]{0.9} %.2f \\%% & \\cellcolor[gray]{0.9} %.4f & \\cellcolor[gray]{0.9} %.4f\\\\\n" %(sample, libplot.prettyInt(stats[0]), libplot.prettyInt(stats[1]), stats[2], stats[3], stats[3]/stats[4]) )
altColor = 1 - altColor
f.write("\\hline\n")
return