def multi_draw(g_pairs, segdata_list, mapfile, idpt, fct_flags, fct_colors, min_size):
"""Draw multiple alignment map with similarity shading."""
print "Lookin\' good!"
# compile info
lengths = [g_pairs[0][0].len+g_pairs[0][0].nudge]
g_to_draw = [g_pairs[0][0]]
for ref, query in g_pairs:
lengths.append(query.len+query.nudge)
g_to_draw.append(query)
max_len = max(lengths)
# calculate main canvas dimensions - horizontal
if max_len*u < 2000:
seq_len = 2000
else:
seq_len = max_len*u
hCan = hmar*4 + pNsize + seq_len
# calculate main canvas dimensions - vertical
vCan = dBL*len(g_pairs) + vmar*4
transX = hmar + pNsize
transY = dBL*len(g_pairs)
init_Y = vmar*2
# set up main canvas
m_canvas = canvasser(hCan, vCan, transX, transY, mapfile)
# draw scale (max_len*u)-pNsize, hmar
seq_scale(m_canvas, 2*hCan/3, -vmar*2, incrT, incrN, dip, dop)
# draw shading legend
heatkey(m_canvas, hCan-hmar*5, init_Y+vmar, idpt)
# draw ref baseline and features
counter = 0
for genome in g_to_draw:
g_record = load_genbank(genome.gbk)
g_feat = g_record.features
g_cds = [feature for feature in g_feat
if feature.type == 'CDS' or feature.type == 'cds']
ref_Y = init_Y-dBL*counter
base_draw(m_canvas, genome, g_cds, '', doLup, ref_Y, 0, 'n', 0,
seq_len, 'n', 'n', fct_flags, fct_colors)
counter +=1
counter = 0
for ref, query in g_pairs:
ref_Y = init_Y-dBL*counter
query_Y = init_Y-dBL*(counter+1)
# draw pairwise similarity shading
try: # TODO: adapt Y
for xa, xb, xc, xd, idp in segdata_list[counter]:
# evaluate color shading category
sh_color = HexColor(simcolor(idp, idpt))
# check for split
if abs(xa) > abs(xb) or abs(xc) > abs(xd):
new_segpairs = shade_split(xa, xb, xc, xd, ref, query)
for xa1, xb1, xc1, xd1 in new_segpairs:
# draw shading
shadowfax(m_canvas, xa1, xb1, xc1, xd1, ref_Y,
query_Y, sh_color, min_size)
else:
# draw shading
shadowfax(m_canvas, xa, xb, xc, xd, ref_Y, query_Y,
sh_color, min_size)
counter +=1
except TypeError:
pass
# write to file and finalize the figure
m_canvas.showPage()
m_canvas.save()
def pairwise_draw(ref, query, segs, map_file, mode1, mode2, annot_mode,
key1, key2, idpt, fct_flags, fct_colors, min_size):
"""Draw pairwise alignment map with similarity shading."""
# load ref record
ref_record = load_genbank(ref.gbk)
ref_feat = ref_record.features
ref_cds = [feature for feature in ref_feat
if feature.type == 'CDS' or feature.type == 'cds']
if annot_mode != 'all':
try:
ref_annot_cds = [1 for cds in ref_cds
if cds.qualifiers.get(key1)[0] !=
'hypothetical protein' and \
cds.qualifiers.get(key1)[0] !=
'no match']
except TypeError:
ref_annot_cds = []
ref_annot_cnt = sum(ref_annot_cds)
else:
ref_annot_cnt = len(ref_cds)
# load query record
query_record = load_genbank(query.gbk)
if query.invert:
query_record = query_record.reverse_complement()
q_feat = query_record.features
query_cds = [feature for feature in q_feat
if feature.type == 'CDS' or feature.type == 'cds']
if annot_mode != 'all':
try:
query_annot_cds = [1 for cds in query_cds
if cds.qualifiers.get(key2)[0] !=
'hypothetical protein' and \
cds.qualifiers.get(key2)[0] !=
'no match']
except TypeError:
query_annot_cds = []
query_annot_cnt = sum(query_annot_cds)
else:
query_annot_cnt = len(query_cds)
# calculate main canvas dimensions - horizontal
if ref.len+ref.nudge > query.len:
ctg_len = ref.len+ref.nudge
else:
ctg_len = query.len
if ctg_len*u < 2000:
seq_len = 2000
else:
seq_len = ctg_len*u
hCan = hmar*2 + pNsize + seq_len
# calculate main canvas dimensions - vertical
if mode1 == 'single' and mode2 == 'n':
annot_cnt = ref_annot_cnt
annot_len = annot_cnt/2
else:
annot_cnt = max(ref_annot_cnt, query_annot_cnt)
annot_len = annot_cnt
vCan = dBL + vmar*6 + annot_len*ck_vsp
transX = hmar + pNsize
transY = dBL + vmar*1.8 + annot_len*ck_vsp
ref_Y = vmar*2.8
query_Y = vmar
# set up main canvas
m_canvas = canvasser(hCan, vCan, transX, transY, map_file)
# draw scale
seq_scale(m_canvas, (ctg_len*u)-pNsize, 0, incrT, incrN, dip, dop )
# draw shading legend
heatkey(m_canvas, -pNsize, -pNsize/2, idpt)
# draw ref baseline and features
base_draw(m_canvas, ref, ref_feat, key1, doLup, ref_Y, 0,
mode1, annot_cnt, seq_len, annot_mode, 'top', fct_flags, fct_colors)
# draw query baseline and features
base_draw(m_canvas, query, q_feat, key2, -doLdn, query_Y, seq_len/2,
mode2, annot_cnt, seq_len, annot_mode, 'low', fct_flags, fct_colors)
# draw pairwise similarity shading
try:
for xa, xb, xc, xd, idp in segs:
# evaluate color shading category
sh_color = HexColor(simcolor(idp, idpt))
# check for split
if abs(xa) > abs(xb) or abs(xc) > abs(xd):
new_segpairs = shade_split(xa, xb, xc, xd, ref, query)
for xa1, xb1, xc1, xd1 in new_segpairs:
# draw shading
shadowfax(m_canvas, xa1, xb1, xc1, xd1, ref_Y, query_Y, sh_color, min_size)
else:
# draw shading
shadowfax(m_canvas, xa, xb, xc, xd, ref_Y, query_Y, sh_color, min_size)
except TypeError:
raise
# write to file and finalize the figure
m_canvas.showPage()
m_canvas.save()
