def load_chromosome(chr_name):
"""Load a chromosome and all of its segments.
"""
cur_chromosome = BasicChromosome.Chromosome(chr_name)
chr_segment_info = all_chr_info[chr_name]
for seg_info_num in range(len(chr_segment_info)):
label, fill_color, scale = chr_segment_info[seg_info_num]
# make the top and bottom telomeres
if seg_info_num == 0:
cur_segment = BasicChromosome.TelomereSegment()
elif seg_info_num == len(chr_segment_info) - 1:
cur_segment = BasicChromosome.TelomereSegment(1)
# otherwise, they are just regular segments
else:
cur_segment = BasicChromosome.ChromosomeSegment()
if label != "":
cur_segment.label = label
if fill_color is not None:
cur_segment.fill_color = fill_color
cur_segment.scale = scale
cur_chromosome.add(cur_segment)
# scale by the size of chromosome 2
cur_chromosome.scale_num = 19
return cur_chromosome
def load_random_chromosome(chr_name):
"""Generate a chromosome with random information about it.
"""
cur_chromosome = BasicChromosome.Chromosome(chr_name)
num_segments = random.randrange(num_possible_segments)
for seg in range(num_segments):
# make the top and bottom telomeres
if seg == 0:
cur_segment = BasicChromosome.TelomereSegment()
elif seg == num_segments - 1:
cur_segment = BasicChromosome.TelomereSegment(1)
# otherwise, they are just regular segments
else:
cur_segment = BasicChromosome.ChromosomeSegment()
color_chance = random.random()
if color_chance <= color_prob:
fill_color = random.choice(color_choices)
cur_segment.fill_color = fill_color
id_chance = random.random()
if id_chance <= id_prob:
id = get_random_id()
cur_segment.label = id
cur_chromosome.add(cur_segment)
return cur_chromosome, num_segments
def test_widget(self):
"""Try widget derived functionality.
"""
test_widget = BasicChromosome.ChromosomeSegment()
expected_string = "chr_percent = 0.25"
# trick to write the properties to a string
save_stdout = sys.stdout
new_stdout = cStringIO.StringIO()
sys.stdout = new_stdout
test_widget.dumpProperties()
properties = new_stdout.getvalue()
sys.stdout = save_stdout
assert properties.find(expected_string) >= 0, \
"Unexpected results from dumpProperties: \n %s" % properties
properties = test_widget.getProperties()
assert properties.has_key("label_size") \
and properties["label_size"] == 6, \
"Unexpected results from getProperties: %s" % properties
test_widget.setProperties({"start_x_position": 12})
assert test_widget.start_x_position == 12, \
"setProperties doesn't seem to work right: %s" \
% test_widget.start_x_position
def drawchrom(cvsfile, write_func, *args):
"""Draw CE chromosome tool.
Doesn't need any parameters.
"""
from Bio.Graphics import BasicChromosome
from reportlab.lib.colors import gray, black
entries = [("chrI", 15072419), ("chrII", 15279316), ("chrIII", 13783681),
("chrIV", 17493784), ("chrV", 20919398), ("chrX", 17718852)]
max_length = max([x[1] for x in entries])
chr_diagram = BasicChromosome.Organism()
for name, length in entries:
cur_chromosome = BasicChromosome.Chromosome(name)
#Set the length, adding and extra 20 percent for the tolomeres:
cur_chromosome.scale_num = max_length * 1.1
# Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = 0.05 * max_length
start.fill_color = black
cur_chromosome.add(start)
#Add a body - using bp as the scale length here.
body = BasicChromosome.ChromosomeSegment()
body.fill_color = gray
body.scale = length
cur_chromosome.add(body)
#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = 0.05 * max_length
end.fill_color = black
cur_chromosome.add(end)
#This chromosome is done
chr_diagram.add(cur_chromosome)
chr_diagram.draw("simple_chrom.pdf", "Caenorhabditis elegans")
def test_widget(self):
"""Try widget derived functionality.
"""
test_widget = BasicChromosome.ChromosomeSegment()
expected_string = "chr_percent = 0.25"
# trick to write the properties to a string
save_stdout = sys.stdout
new_stdout = StringIO()
sys.stdout = new_stdout
test_widget.dumpProperties()
properties = new_stdout.getvalue()
sys.stdout = save_stdout
self.assertTrue(
expected_string in properties,
"Unexpected results from dumpProperties: \n %s" % properties)
properties = test_widget.getProperties()
self.assertEqual(
properties["label_size"], 6,
"Unexpected results from getProperties: %s" % properties)
test_widget.setProperties({"start_x_position": 12})
self.assertEqual(
test_widget.start_x_position, 12,
"setProperties doesn't seem to work right: %s" %
test_widget.start_x_position)
def draw_chromosome(sequence):
entries = [("Legionella Pneumophilia")]
max_len = 30432563
telomere_length = 1000000
chr_diagram = BasicChromosome.Organism()
chr_diagram.page_size = (29.7*cm, 21*cm) #A4 landscape
for name, length in entries:
cur_chromosome = BasicChromosome.Chromosome(name)
cur_chromosome.scale_num = max_len + 2 * telomere_length
start = BasicChromosome.TelomereSegment()
start.scale = telomere_length
cur_chromosome.add(start)
body = BasicChromosome.ChromosomeSegment()
body.scale = length
cur_chromosome.add(body)
end = BasicChromosome.TelomereSegement(inverted=True)
end.scale = telomere_length
cur_chromosome.add(end)
chr_diagram.add(cur_chromosome)
chr_diagram.draw("Chromosome.pdf", "Legionella Pneumophilia")
def load_chrom(chr_name):
""" Generate a chromosome with information
"""
cur_chromosome = BasicChromosome.Chromosome(chr_name[0])
chr_segment_info = chr_name[1]
for seg_info_num in range(len(chr_segment_info)):
label, color, scale = chr_segment_info[seg_info_num]
# make the top and bottom telomeres
if seg_info_num == 0:
cur_segment = BasicChromosome.TelomereSegment()
elif seg_info_num == len(chr_segment_info) - 1:
cur_segment = BasicChromosome.TelomereSegment(1)
# otherwise, they are just regular segments
else:
cur_segment = BasicChromosome.ChromosomeSegment()
cur_segment.label = label
cur_segment.label_size = 12
cur_segment.fill_color = color
cur_segment.scale = scale
cur_chromosome.add(cur_segment)
cur_chromosome.scale_num = max(END) + (max(END) * .04)
return cur_chromosome
def get(self): #查找和查询
s=entity.hosInfo(self.db)
#cent_code='004'
offset = int(self.get_argument('o',default='1'))
rowcount = int(self.get_argument('r',default='10'))
offset=(offset-1)*rowcount
no=self.get_argument("no",default='')
file_id=self.get_argument("file_id",default='')
cur=self.db.getCursor()
if no=='1':
sql="select a.path from public.file a where a.id=%s "%(file_id)
cur.execute(sql)
row = cur.fetchone()
rowdata={}
rowdata['rows']=row
print(row)
filename="/home/ubuntu/pythonff/mdt/mdt/mdtproject/trunk/app/"+row[0]
imgfile=filename[:-2]+"svg"
imgfile1=filename[:-2]+"1.svg"
print(filename)
print(imgfile)
record = SeqIO.read(filename, "genbank")
gd_diagram = GenomeDiagram.Diagram(record.id)
gd_track_for_features = gd_diagram.new_track(1, name="Annotated Features")
gd_feature_set = gd_track_for_features.new_set()
for feature in record.features:
if feature.type != "gene":
#Exclude this feature
continue
if len(gd_feature_set) % 2 == 0:
color = colors.blue
else:
color = colors.lightblue
gd_feature_set.add_feature(feature, sigil="ARROW",
color=color, label=True,
label_size = 14, label_angle=0)
#I want to include some strandless features, so for an example
#will use EcoRI recognition sites etc.
for site, name, color in [("GAATTC","EcoRI",colors.green),
("CCCGGG","SmaI",colors.orange),
("AAGCTT","HindIII",colors.red),
("GGATCC","BamHI",colors.purple)]:
index = 0
while True:
index = record.seq.find(site, start=index)
if index == -1 : break
feature = SeqFeature(FeatureLocation(index, index+len(site)))
gd_feature_set.add_feature(feature, color=color, name=name,
label=True, label_size = 10,
label_color=color)
index += len(site)
gd_diagram.draw(format="linear", pagesize='A4', fragments=4,
start=0, end=len(record))
#gd_diagram.write("plasmid_linear_nice.pdf", "PDF")
#gd_diagram.write("plasmid_linear_nice.eps", "EPS")
gd_diagram.write(imgfile, "SVG")
gd_diagram.draw(format="circular", circular=True, pagesize=(20*cm,20*cm),
start=0, end=len(record), circle_core = 0.5)
#gd_diagram.write("plasmid_circular_nice.pdf", "PDF")
#gd_diagram.write("plasmid_circular_nice.eps", "EPS")
gd_diagram.write(imgfile1, "SVG")
elif no=='2':
q=0
pdffile="/home/ubuntu/pythonff/mdt/mdt/mdtproject/trunk/app/uploads/tm/"+file_id+".pdf"
pdf="uploads/tm/"+file_id+".pdf"
file_id=file_id.split(',')
sql1="where a.id=%s "%(file_id[q])
for i in range(len(file_id)-1):
sql1=sql1+"or a.id=%s "%(file_id[q+1])
q=q+1
sql="select a.path,a.file_name from public.file a %s "%(sql1)
cur.execute(sql)
row = cur.fetchall()
print(row)
rowdata={}
rowdata['rows']=pdf
q=0
a=[]
entriess = []
entries = []
for i in range(len(row)):
filepath="/home/ubuntu/pythonff/mdt/mdt/mdtproject/trunk/app/"+row[q][0]
filename=row[q][1]
entriess.append((filename,filepath))
q=q+1
for(name,path) in entriess:
record=SeqIO.read(path,"fasta")
a.append(len(record))
entries.append((name,len(record)))
max_len = max(a)
telomere_length = 1000000 #For illustration
chr_diagram = BasicChromosome.Organism()
chr_diagram.page_size = (29.7*cm, 21*cm) #A4 landscape
for name, length in entries:
cur_chromosome = BasicChromosome.Chromosome(name)
#Set the scale to the MAXIMUM length plus the two telomeres in bp,
#want the same scale used on all five chromosomes so they can be
#compared to each other
cur_chromosome.scale_num = max_len + 2 * telomere_length
#Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = telomere_length
cur_chromosome.add(start)
#Add a body - using bp as the scale length here.
body = BasicChromosome.ChromosomeSegment()
body.scale = length
cur_chromosome.add(body)
#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = telomere_length
cur_chromosome.add(end)
#This chromosome is done
chr_diagram.add(cur_chromosome)
chr_diagram.draw(pdffile, "Arabidopsis thaliana")
elif no=='3':
q=0
pdffile="/home/ubuntu/pythonff/mdt/mdt/mdtproject/trunk/app/uploads/tm/"+file_id+".pdf"
pdf="uploads/tm/"+file_id+".pdf"
file_id=file_id.split(',')
sql1="where a.id=%s "%(file_id[q])
for i in range(len(file_id)-1):
sql1=sql1+"or a.id=%s "%(file_id[q+1])
q=q+1
sql="select a.path,a.file_name from public.file a %s "%(sql1)
cur.execute(sql)
row = cur.fetchall()
print(row)
rowdata={}
rowdata['rows']=pdf
q=0
a=[]
entries = []
for i in range(len(row)):
filepath="/home/ubuntu/pythonff/mdt/mdt/mdtproject/trunk/app/"+row[q][0]
filename=row[q][1]
entries.append((filename,filepath))
q=q+1
for(name,path) in entries:
record=SeqIO.read(path,"genbank")
a.append(len(record))
max_len=max(a)
telomere_length = 1000000 #For illustration
chr_diagram = BasicChromosome.Organism()
chr_diagram.page_size = (29.7*cm, 21*cm) #A4 landscape
for index, (name, filename) in enumerate(entries):
record = SeqIO.read(filename,"genbank")
length = len(record)
features = [f for f in record.features if f.type=="tRNA"]
#Record an Artemis style integer color in the feature's qualifiers,
#1 = Black, 2 = Red, 3 = Green, 4 = blue, 5 =cyan, 6 = purple
for f in features: f.qualifiers["color"] = [index+2]
cur_chromosome = BasicChromosome.Chromosome(name)
#Set the scale to the MAXIMUM length plus the two telomeres in bp,
#want the same scale used on all five chromosomes so they can be
#compared to each other
cur_chromosome.scale_num = max_len + 2 * telomere_length
#Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = telomere_length
cur_chromosome.add(start)
#Add a body - again using bp as the scale length here.
body = BasicChromosome.AnnotatedChromosomeSegment(length, features)
body.scale = length
cur_chromosome.add(body)
#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = telomere_length
cur_chromosome.add(end)
#This chromosome is done
chr_diagram.add(cur_chromosome)
chr_diagram.draw(pdffile, "Arabidopsis thaliana")
self.response(rowdata)
def combcall2draw(cvsfile, write_func, *args):
"""User specifies several columns to consider, this tool will call
regions where either of the column is above its threshold.
"""
argv = args[0]
if len(argv) < 6:
sys.stderr.write(
"Need 6 extra arguments for 'combcall2draw', options <loc column> <score column1[,score column2,...]> <cutoff1[,cutoff2,cutoff3]> <min length> <max gap> <pdf filename>\ne.g. command: <0> <1,2,3> <0.5,0.6,0.7> <10000> <2000> <a.pdf>, means to use the first column as genome coordinations to call enriched regions from the combinition of #1, #2 and #3, the thresholds to call enriched region are 0.5 for column 1, 0.6 for column 2 and 0.7 for column 3, the minimum length of region is 10k, and the maximum gap to link two nearby regions is 2k. Then the figure will be saved in a.pdf.\n"
)
sys.exit()
cor_column = cvsfile.fieldnames[int(argv[0])]
var_columns = map(lambda x: cvsfile.fieldnames[int(x)], argv[1].split(","))
cutoffs = map(float, argv[2].split(","))
min_len = int(argv[3])
max_gap = int(argv[4])
wtrack = WigTrackI(
) # combined track containing 1 if either of track is above cutoff
add_func = wtrack.add_loc
for l in cvsfile:
cor = l.setdefault(cor_column, None)
if not cor or cor == "NA":
continue
for i in range(len(var_columns)):
var_column = var_columns[i]
cutoff = cutoffs[i]
var = l.setdefault(var_column, None)
if var and var != "NA" and float(var) > cutoff:
(chrom, start, end) = cor.split(".")
add_func(chrom, int(start), 1.1)
break
wtrack.span = int(end) - int(start)
bpeaks = wtrack.call_peaks(cutoff=1.0, min_length=min_len, max_gap=max_gap)
#f = argv[5]
fhd = open(argv[5].replace("pdf", "bed"), "w")
fhd.write(bpeaks.tobed())
from Bio.Graphics import BasicChromosome
from reportlab.lib.colors import gray, black, white
entries = [("chrI", 15072419), ("chrII", 15279316), ("chrIII", 13783681),
("chrIV", 17493784), ("chrV", 20919398), ("chrX", 17718852)]
max_length = max([x[1] for x in entries])
chr_diagram = BasicChromosome.Organism()
for name, length in entries:
cur_chromosome = BasicChromosome.Chromosome(name)
#Set the length, adding and extra 20 percent for the tolomeres:
cur_chromosome.scale_num = max_length * 1.1
# Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = 0.05 * max_length
start.fill_color = gray
cur_chromosome.add(start)
#Add a body - using bp as the scale length here.
try:
cpeaks = bpeaks.peaks[name]
except:
cpeaks = []
body_regions = []
last_pos = 0
for p in cpeaks:
body_regions.append((p[0] - last_pos, white)) # outside regions
body_regions.append((p[1] - p[0], black)) # enriched regions
last_pos = p[1]
assert p[1] < length
body_regions.append((length - last_pos, white)) # last part
for b, c in body_regions:
body = BasicChromosome.ChromosomeSegment()
body.fill_color = c
body.scale = b
cur_chromosome.add(body)
#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = 0.05 * max_length
end.fill_color = gray
cur_chromosome.add(end)
#This chromosome is done
chr_diagram.add(cur_chromosome)
chr_diagram.draw(argv[5], "Highlight regions in Caenorhabditis elegans")
def call1draw(cvsfile, write_func, *args):
"""Call regions, then plot it in chromosome figure.
A combination of drawchrom and call1
"""
argv = args[0]
if len(argv) < 6:
sys.stderr.write(
"Need 6 extra arguments for 'call1draw', options <loc column> <score column> <cutoff> <min length> <max gap> <pdf filename>\ne.g. command: <0> <1> <0.5> <10000> <2000> <a.pdf>, means to use the first column as genome coordinations to call enriched regions from the second column, the threshold to call enriched region is 0.5, the minimum length of region is 10k, and the maximum gap to link two nearby regions is 2k. Then the figure will be saved in a.pdf.\n"
)
sys.exit()
cor_column = cvsfile.fieldnames[int(argv[0])]
var_column = cvsfile.fieldnames[int(argv[1])]
cutoff = float(argv[2])
min_len = int(argv[3])
max_gap = int(argv[4])
wtrack = WigTrackI()
add_func = wtrack.add_loc
for l in cvsfile:
cor = l.setdefault(cor_column, None)
var = l.setdefault(var_column, None)
if cor and var and cor != "NA" and var != "NA":
(chrom, start, end) = cor.split(".")
add_func(chrom, int(start), float(var))
wtrack.span = int(end) - int(start)
bpeaks = wtrack.call_peaks(cutoff=cutoff,
min_length=min_len,
max_gap=max_gap)
fhd = open(argv[5].replace("pdf", "bed"), "w")
fhd.write(bpeaks.tobed())
from Bio.Graphics import BasicChromosome
from reportlab.lib.colors import gray, black, white
entries = [("chrI", 15072419), ("chrII", 15279316), ("chrIII", 13783681),
("chrIV", 17493784), ("chrV", 20919398), ("chrX", 17718852)]
max_length = max([x[1] for x in entries])
chr_diagram = BasicChromosome.Organism()
for name, length in entries:
cur_chromosome = BasicChromosome.Chromosome(name)
#Set the length, adding and extra 20 percent for the tolomeres:
cur_chromosome.scale_num = max_length * 1.1
# Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = 0.05 * max_length
start.fill_color = gray
cur_chromosome.add(start)
#Add a body - using bp as the scale length here.
try:
cpeaks = bpeaks.peaks[name]
except:
cpeaks = []
body_regions = []
last_pos = 0
for p in cpeaks:
body_regions.append((p[0] - last_pos, white)) # outside regions
body_regions.append((p[1] - p[0], black)) # enriched regions
last_pos = p[1]
assert p[1] < length
body_regions.append((length - last_pos, white)) # last part
for b, c in body_regions:
body = BasicChromosome.ChromosomeSegment()
body.fill_color = c
body.scale = b
cur_chromosome.add(body)
#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = 0.05 * max_length
end.fill_color = gray
cur_chromosome.add(end)
#This chromosome is done
chr_diagram.add(cur_chromosome)
chr_diagram.draw(argv[5],
"%s regions in Caenorhabditis elegans" % (var_column))
chr_diagram.page_size = (29.7 * cm, 21 * cm) #A4 landscape
for name, length in entries:
cur_chromosome = BasicChromosome.Chromosome(name)
#Set the scale to the MAXIMUM length plus the two telomeres in bp,
#want the same scale used on all five chromosomes so they can be
#compared to each other
cur_chromosome.scale_num = max_len + 2 * telomere_length
#Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = telomere_length
cur_chromosome.add(start)
#Add a body - using bp as the scale length here.
body = BasicChromosome.ChromosomeSegment()
body.scale = length
cur_chromosome.add(body)
#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = telomere_length
cur_chromosome.add(end)
#This chromosome is done
chr_diagram.add(cur_chromosome)
os.chdir('C:\\Users\\qxs\\Documents\\Python Scripts')
chr_diagram.draw("Brapa_chrom.pdf", "Brassica rapa")
###### simcoal2
def main():
from taolib.CoreLib.Parser.BedIO import parse_BED
from Bio.Graphics import BasicChromosome
if len(sys.argv) < 3:
sys.stderr.write(
"Draw Chromosome Figure\nneed 2 paras: %s <dbname> <color> <bed file>\n"
% sys.argv[0])
sys.exit(1)
try:
entries = get_chrom_length(sys.argv[1])
except:
error("Error!")
sys.exit(1)
col = getCol(sys.argv[2])
bpeaks = parse_BED(open(sys.argv[3]))
pdffile = sys.argv[3] + ".pdf"
max_length = max([x[1] for x in entries])
chr_diagram = BasicChromosome.Organism()
for name, length in entries:
cur_chromosome = BasicChromosome.Chromosome(name)
cur_chromosome.title_size = 0.5
#Set the length, adding and extra 20 percent for the tolomeres:
cur_chromosome.scale_num = max_length * 1.1
# Add an opening telomere
start = BasicChromosome.TelomereSegment()
start.scale = 0.05 * max_length
start.fill_color = gray
cur_chromosome.add(start)
#Add a body - using bp as the scale length here.
try:
cpeaks = bpeaks.peaks[name]
except:
cpeaks = []
body_regions = []
last_pos = 0
for p in cpeaks:
body_regions.append((p[0] - last_pos, white)) # outside regions
body_regions.append((p[1] - p[0], col)) # enriched regions
last_pos = p[1]
assert p[1] < length
body_regions.append((length - last_pos, white)) # last part
for b, c in body_regions:
body = BasicChromosome.ChromosomeSegment()
body.fill_color = c
body.scale = b
cur_chromosome.add(body)
#Add a closing telomere
end = BasicChromosome.TelomereSegment(inverted=True)
end.scale = 0.05 * max_length
end.fill_color = gray
cur_chromosome.add(end)
#This chromosome is done
chr_diagram.add(cur_chromosome)
chr_diagram.draw(pdffile, "Highlight regions")
