def get_phage_name_from_PhageID(self, PhageID):
self.c = db_conf.db_conf(username=self.username,
password=self.password,
server=self.server,
db=self.database).get_cursor()
self.db = pham.db(c=self.c)
return phamerator_manage_db.get_phage_name_from_PhageID(
self.c, PhageID)
def create_pham_circle(self,phamName,alignmentColor,adjustment,radius):
self.c = db_conf.db_conf(username=self.username,password=self.password,server=self.server,db=self.database).get_cursor()
self.db = pham.db(c = self.c)
filename = str(phamName) + str(alignmentColor) + str(adjustment) + str(radius)
filelist = os.listdir(self.cachedir)
for item in filelist:
if item == filename:
self.current_phamCircle = self.cachedir + filename
string = "phamCircle " + str(phamName) + " found in cache, using cached version\n"
print ">" + string
return string
self.radius = radius
self.alignmentColor = alignmentColor
self.threshold = 0.70
self.phamCircleCanvas = goocanvas.Canvas()
GeneIDs = phamerator_manage_db.get_members_of_pham(self.c, phamName)
memberPhages, self.nonMemberPhages = [], []
for GeneID in GeneIDs:
PhageID = phamerator_manage_db.get_PhageID_from_GeneID(self.c, GeneID)
if PhageID not in memberPhages: memberPhages.append(PhageID)
totalPhages = phamerator_manage_db.get_PhageIDs(self.c)
for p in totalPhages:
if p not in memberPhages: self.nonMemberPhages.append(phamerator_manage_db.get_phage_name_from_PhageID(self.c, p))
self.l = []
self.genes = []
for a in GeneIDs:
for b in GeneIDs:
if a != b:
for gene in [a, b]:
if gene not in self.genes: self.genes.append(gene)
clustalwScore, blastScore = phamerator_manage_db.get_scores(self.c, a, b)
if clustalwScore >= 0.275: self.l.append((a, b, 'clustalw',clustalwScore))
if blastScore and blastScore <= 0.0001: self.l.append((a, b, 'blast',blastScore))
self.phamCircle = PhamDisplay.PhamCircle(phamName, self.c,verbose=True,radius=self.radius)
if self.alignmentColor == True:
self.phamCircleCanvas.set_root_item_model(self.phamCircle.create_canvas_model(self.nonMemberPhages, self.genes, self.l,adjustment,self.threshold,blastColor='#ff0000', clustalwColor='#0000ff'))
else:
phamColorFromDataBase = self.db.select('pham_color','color',name = phamName)[0][0]
self.phamCircleCanvas.set_root_item_model(self.phamCircle.create_canvas_model(self.nonMemberPhages, self.genes, self.l,adjustment,self.threshold,allColor = phamColorFromDataBase))
"""x, y = (600, 500)
self.phamCircleCanvas.set_size_request(x, y)
self.defaultPhamCircleCanvasSize = (x, y)
self.phamCircleCanvas.show()
self.window.window.set_cursor(None)
return False"""
self.current_phamCircle = self.cachedir + filename
self.phamCircleCanvas.set_bounds(0,0, 10000, 10000)
surface = cairo.SVGSurface (self.current_phamCircle, 15*72, 15*72)
cr = cairo.Context (surface)
cr.translate (10, 0)
self.phamCircleCanvas.render (cr, None, 0.1)
cr.show_page()
string = "phamCircle " + str(phamName) + " generated\n"
print ">" + string
return string
def get_phage_name_from_PhageID(self, PhageID): self.c = db_conf.db_conf(username=self.username,password=self.password,server=self.server,db=self.database).get_cursor() self.db = pham.db(c = self.c) return phamerator_manage_db.get_phage_name_from_PhageID(self.c, PhageID)
def create_pham_circle(self, phamName, alignmentColor, adjustment, radius):
self.c = db_conf.db_conf(username=self.username,
password=self.password,
server=self.server,
db=self.database).get_cursor()
self.db = pham.db(c=self.c)
filename = str(phamName) + str(alignmentColor) + str(adjustment) + str(
radius)
filelist = os.listdir(self.cachedir)
for item in filelist:
if item == filename:
self.current_phamCircle = self.cachedir + filename
string = "phamCircle " + str(
phamName) + " found in cache, using cached version\n"
print ">" + string
return string
self.radius = radius
self.alignmentColor = alignmentColor
self.threshold = 0.70
self.phamCircleCanvas = goocanvas.Canvas()
GeneIDs = phamerator_manage_db.get_members_of_pham(self.c, phamName)
memberPhages, self.nonMemberPhages = [], []
for GeneID in GeneIDs:
PhageID = phamerator_manage_db.get_PhageID_from_GeneID(
self.c, GeneID)
if PhageID not in memberPhages: memberPhages.append(PhageID)
totalPhages = phamerator_manage_db.get_PhageIDs(self.c)
for p in totalPhages:
if p not in memberPhages:
self.nonMemberPhages.append(
phamerator_manage_db.get_phage_name_from_PhageID(
self.c, p))
self.l = []
self.genes = []
for a in GeneIDs:
for b in GeneIDs:
if a != b:
for gene in [a, b]:
if gene not in self.genes: self.genes.append(gene)
clustalwScore, blastScore = phamerator_manage_db.get_scores(
self.c, a, b)
if clustalwScore >= 0.275:
self.l.append((a, b, 'clustalw', clustalwScore))
if blastScore and blastScore <= 0.0001:
self.l.append((a, b, 'blast', blastScore))
self.phamCircle = PhamDisplay.PhamCircle(phamName,
self.c,
verbose=True,
radius=self.radius)
if self.alignmentColor == True:
self.phamCircleCanvas.set_root_item_model(
self.phamCircle.create_canvas_model(self.nonMemberPhages,
self.genes,
self.l,
adjustment,
self.threshold,
blastColor='#ff0000',
clustalwColor='#0000ff'))
else:
phamColorFromDataBase = self.db.select('pham_color',
'color',
name=phamName)[0][0]
self.phamCircleCanvas.set_root_item_model(
self.phamCircle.create_canvas_model(
self.nonMemberPhages,
self.genes,
self.l,
adjustment,
self.threshold,
allColor=phamColorFromDataBase))
"""x, y = (600, 500)
self.phamCircleCanvas.set_size_request(x, y)
self.defaultPhamCircleCanvasSize = (x, y)
self.phamCircleCanvas.show()
self.window.window.set_cursor(None)
return False"""
self.current_phamCircle = self.cachedir + filename
self.phamCircleCanvas.set_bounds(0, 0, 10000, 10000)
surface = cairo.SVGSurface(self.current_phamCircle, 15 * 72, 15 * 72)
cr = cairo.Context(surface)
cr.translate(10, 0)
self.phamCircleCanvas.render(cr, None, 0.1)
cr.show_page()
string = "phamCircle " + str(phamName) + " generated\n"
print ">" + string
return string
