def getAllStatsLatexTab(sampleToExps, cutoff, outfile, sampleOrder):
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
tabHeader2(f)
tab2(f, sampleToExps, cutoff, sampleOrder)
label = ''
captionStr = ''
iseqlib.tableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def getTab(outfile, colnames, sample2row):
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
myTabHeader(f, colnames[1:])
tab(f, colnames, sample2row)
label = ''
captionStr = ''
iseqlib.tableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def getTab(outfile, rows):
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
myTabHeader(f)
tab(f, rows)
label = ''
captionStr = ''
iseqlib.tableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def printTexTab0(clones, clone2hits, group2keywords, options, outbasename):
outfile = "%s.tex" %outbasename
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
myTabHeader(f)
tab(f, clones, clone2hits, group2keywords, options)
label = ''
captionStr = ''
iseqlib.tableCloser(f, captionStr, label)
#iseqlib.sidewaystableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def printTexTab(clones, clone2hits, group2keywords, options, outdir):
outfile = os.path.join(outdir, 'hits.tex')
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
myTabHeader(f)
tab(f, clones, clone2hits, group2keywords, options)
label = ''
captionStr = ''
iseqlib.tableCloser(f, captionStr, label)
#iseqlib.sidewaystableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def printTexTab(clones, clone2hits, group2keywords, options, outbasename):
outfile = "%s.tex" %outbasename
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
samples = ['AS1', 'AS2', 'AS3', 'AS4', 'AS5', 'H1', 'H2']
myTabHeader(f, samples)
tab(f, clones, clone2hits, group2keywords, options, samples)
label = ''
captionStr = ''
#iseqlib.tableCloser(f, captionStr, label)
iseqlib.sidewaystableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def getLatexTab(outfile, rowname2cells, index2colname):
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
colnames = []
for i in sorted( index2colname.keys() ):
colnames.append( index2colname[i] )
tabHeader(f, colnames)
tab(f, rowname2cells, index2colname)
label = ''
captionStr = ''
iseqlib.tableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def printTexTab(clones, clone2hits, group2keywords, options, outbasename):
outfile = "%s.tex" % outbasename
f = open(outfile, "w")
iseqlib.writeDocumentStart(f)
samples = ["AS1", "AS2", "AS3", "AS4", "AS5", "H1", "H2"]
myTabHeader(f, samples)
tab(f, clones, clone2hits, group2keywords, options, samples)
label = ""
captionStr = ""
# iseqlib.tableCloser(f, captionStr, label)
iseqlib.sidewaystableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def getClonesizeLatexTab(samples, groupsamples, group2samples, outfile, simpson):
f = open(outfile, 'w')
iseqlib.writeDocumentStart(f)
tabHeader(f, simpson)
tab(f, samples, groupsamples, group2samples, simpson)
label = ''
captionStr = "TCRB sequence statistics. Columns: `Sample': sample name, `Clones': number of unique clones, `Total Reads': number of total reads. Rows: different samples, where the shaded rows show the average of statistics of each group."
if simpson:
captionStr = "TCRB sequence statistics. Columns: `Sample': sample name, `Clones': number of unique clones, `Total Reads': number of total reads, `Simpson Index': Simpson diversity index, which is equivalent with the probability that any two sequences (reads) belong to two different clones. Rows: different samples, where the shaded rows show the average of statistics of each group."
iseqlib.tableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
def getCutoffsLatexTab(exps, file, statsType, sampleOrder):
if len(exps) == 0:
return
cutoffs = exps[0].cutoffs
for exp in exps:
for i, c in enumerate(exp.cutoffs):
if c != cutoffs[i]:
raise InconsistentCutoffsError("Input files don't have the same cutoffs.")
f = open(file, 'w')
iseqlib.writeDocumentStart(f)
#Table:
cutoffs = exps[0].cutoffs
tabHeader(f, cutoffs)
tab(f, exps, statsType, sampleOrder)
label = ''
captionStr = ''
iseqlib.tableCloser(f, captionStr, label)
iseqlib.writeDocumentEnd(f)
f.close()
#---- main -----
field2index = {'%Cutoff':0, 'Clones1':1, 'Clones2':2, 'Overlap1':3, 'Overlap2':4, '%1overlap2':5, '%2overlap1':6, '%reads1overlap2':7, '%reads2overlap1':8}
cutoff2line = {}
for line in sys.stdin:
line = line.strip('\n')
if len(line) == 0:
continue
if line[0] == '#':
line = line.lstrip('#')
items = line.split('\t')
for i, item in enumerate(items):
field2index[item] = i
else:
items = line.split('\t')
cutoffIndex = field2index['%Cutoff']
cutoff = float(items[cutoffIndex])
cutoff2line[cutoff] = line
iseqlib.writeDocumentStart(sys.stdout)
tabHeader(sys.stdout)
tab(sys.stdout, cutoff2line, field2index)
label=''
captionStr = ''
iseqlib.sidewaystableCloser(sys.stdout, captionStr, label)
iseqlib.writeDocumentEnd(sys.stdout)
