def tab0(f, clones, clone2hits, group2keywords, options):
for clone in clones:
vs, js, ds, sample2size = getCloneInfo(clone)
if clone in clone2hits:
hits = clone2hits[clone]
hitsWithKeyword = [] # list of hits that have at least 1 keyword
for hit in hits:
for g, kw in group2keywords.iteritems():
if g == "b27" or g == "pathogen":
continue
if checkKeywords(hit[0], kw):
hitsWithKeyword.append(hit)
break
if len(hitsWithKeyword) == 0: # no hit with keyword
continue
seq = hits[0][2]
samples = sorted([iseqlib.properName(s) for s in sample2size.keys()])
numrow = max([len(samples), len(hitsWithKeyword)])
f.write(
"\\multirow{%d}{*}{%s} & \\multirow{%d}{*}{%s} & \\multirow{%d}{*}{%s} & "
% (numrow, vs, numrow, seq, numrow, js)
) # Write V, CDR3, J
# f.write("%s & %d & %s & %s & %s \\\\\n " %( samples[0], sample2size[iseqlib.properName2name(samples[0])], hitsWithKeyword[0][4], hitsWithKeyword[0][3], hitsWithKeyword[0][0] )) #first row
f.write(
"%s & %d & %s & %s & %s \\\\\n "
% (
samples[0],
sample2size[iseqlib.properName2name(samples[0])],
hitsWithKeyword[0][4],
hitsWithKeyword[0][3],
parsePaperInfo(hitsWithKeyword[0][0]),
)
)
for i in xrange(1, numrow):
f.write("\\cline{4-8}\n")
f.write(" & & & ")
if i < len(samples):
s = samples[i]
f.write(" %s & %d &" % (s, sample2size[iseqlib.properName2name(s)]))
else:
f.write(" & & ")
if i < len(hitsWithKeyword):
h = hitsWithKeyword[i]
# f.write( "%s & %s & %s \\\\\n" %(h[4], h[3], h[0]) )
f.write("%s & %s & %s \\\\\n" % (h[4], h[3], parsePaperInfo(h[0])))
else:
f.write(" & & \\\\\n")
f.write("\\hline\n")
def tab(f, clones, clone2hits, group2keywords, options, samples):
for clone in clones:
vs, js, ds, sample2size = getCloneInfo(clone)
if clone in clone2hits:
hits = clone2hits[clone]
hitsWithKeyword = [] # list of hits that have at least 1 keyword
for hit in hits:
for g, kw in group2keywords.iteritems():
if g == "b27" or g == "pathogen":
continue
if checkKeywords(hit[0], kw):
hitsWithKeyword.append(hit)
break
if len(hitsWithKeyword) == 0: # no hit with keyword
continue
seq = hits[0][2]
numrow = len(hitsWithKeyword)
# First line
f.write(
"\\multirow{%d}{*}{%s} & \\multirow{%d}{*}{%s} & \\multirow{%d}{*}{%s} & "
% (numrow, vs, numrow, seq, numrow, js)
) # Write V, CDR3, J
for s in samples:
name = iseqlib.properName2name(s)
if name in sample2size:
count = sample2size[name]
f.write("\\multirow{%d}{*}{%d} & " % (numrow, count))
else:
f.write("\\multirow{%d}{*}{} & " % (numrow))
f.write(
"%s & %s & %s \\\\\n "
% (hitsWithKeyword[0][4], hitsWithKeyword[0][3], parsePaperInfo(hitsWithKeyword[0][0]))
)
# Other hits:
for i in xrange(1, numrow):
f.write("\\cline{%d-%d}\n" % (3 + len(samples) + 1, 3 + len(samples) + 3))
f.write(" &" * (3 + len(samples)))
h = hitsWithKeyword[i]
f.write("%s & %s & %s \\\\\n" % (h[4], h[3], parsePaperInfo(h[0])))
f.write("\\hline\n")
def tab(f, clones, clone2hits, group2keywords, options, samples):
for clone in clones:
vs, js, ds, sample2size = getCloneInfo(clone)
if clone in clone2hits:
hits = clone2hits[clone]
hitsWithKeyword = [] #list of hits that have at least 1 keyword
for hit in hits:
if checkKeywords(hit.title, group2keywords['mice']) or (options.abstract and checkKeywords(hit.abstract, group2keywords['mice'])): #mice studies, ignore
continue
for g, kw in group2keywords.iteritems():
if g == 'b27' or g == 'pathogen':
continue
if checkKeywords(hit.title, kw) or (options.abstract and checkKeywords(hit.abstract, kw)):
hitsWithKeyword.append(hit)
break
if len(hitsWithKeyword) == 0: #no hit with keyword
continue
seq = hits[0].qAln
numrow = len(hitsWithKeyword)
#First line
f.write("\\multirow{%d}{*}{%s} & \\multirow{%d}{*}{%s} & \\multirow{%d}{*}{%s} & " %(numrow, vs, numrow, seq, numrow, js) ) #Write V, CDR3, J
for s in samples:
name = iseqlib.properName2name(s)
if name in sample2size:
count = sample2size[name]
f.write("\\multirow{%d}{*}{%d} & " % (numrow, count))
else:
f.write("\\multirow{%d}{*}{} & " % (numrow))
f.write("%s & %s & %s \\\\\n " %( hitsWithKeyword[0].tAln, hitsWithKeyword[0].match, parsePaperInfo(hitsWithKeyword[0].title) ))
#Other hits:
for i in xrange(1, numrow):
f.write("\\cline{%d-%d}\n" %(3 + len(samples) + 1, 3 + len(samples) + 3))
f.write(" &"*( 3 + len(samples) ) )
h = hitsWithKeyword[i]
f.write( "%s & %s & %s \\\\\n" %(h.tAln, h.match, parsePaperInfo(h.title)) )
f.write("\\hline\n")
