def usageTab(types, sample, avrstats, stdstats, type2genelist, outdir):
for type in types:
avrgene2count = {}
stdgene2count = {}
totalreads = 0
totaluniqs = 0
if type in avrstats:
avrgene2count = avrstats[type]
stdgene2count = stdstats[type]
totalreads = sum([counts[0] for counts in avrgene2count.values()])
totaluniqs = sum([counts[1] for counts in avrgene2count.values()])
#if totalreads == 0 or totaluniqs == 0:
# raise ValueError("sample with zero read/sequence")
if type in type2genelist:
genes = type2genelist[type]
else:
genes = sorted( avrgene2count.keys() )
typedir = os.path.join(outdir, type)
outfile = os.path.join(typedir, "%s-%s.txt" %(sample, type) )
f = open(outfile, 'w')
f.write("Gene\tReads\t%Reads\tUniq\t%uniq\tStdReads\tStdUniq\n")
#numpass = 0
for g in genes:
if g not in avrgene2count:
sys.stderr.write("Gene %s is not in avrgene2count %s\n" %(g, ','.join(avrgene2count.keys()) ))
avrcounts = [0.0, 0.0]
stdcounts = [0.0, 0.0]
else:
#numpass += 1
avrcounts = avrgene2count[g]
stdcounts = stdgene2count[g]
read = avrcounts[0]
uniq = avrcounts[1]
readPc = 0.0
uniqPc = 0.0
if totalreads > 0:
readPc = iseqlib.getPc(read, totalreads)
if totaluniqs > 0:
uniqPc = iseqlib.getPc(uniq, totaluniqs)
f.write("%s\t%d\t%f\t%d\t%f\t%d\t%d\n" %(g, read, readPc, uniq, uniqPc, stdcounts[0], stdcounts[1]))
f.close()
def tab(f, colnames, sample2row):
#Print total:
totalRow = sample2row['Total']
f.write("%s & %s \\\\\n" % ("Total", " & ".join( ["%s & 100.00" %cell for cell in totalRow] )) )
f.write("\\hline\n")
for sample in sorted(sample2row.keys()):
if sample == 'Total' or sample == 'controls' or sample == 'patients' :
continue
f.write("%s" % iseqlib.properName(sample))
row = sample2row[sample]
for i, cell in enumerate(row):
total = totalRow[i]
pc = iseqlib.getPc( int(cell), int(total) )
f.write( " & %s & %.2f " %(cell, pc) )
f.write("\\\\\n")
f.write("\\hline\n")
