def actionPerformed(self, event):
output = open("profelis.query.fas", "w")
for gene in self.panel.outGenes.model.elements():
print gene.location
if gene.location[0] < gene.location[1]:
proteins = utils.translate(self.panel.genome[gene.location[0]-1:gene.location[1]])
else:
proteins = utils.translate(utils.reverseComplement(self.panel.genome[gene.location[1]-1:gene.location[0]]))
output.write(">profelis" + ":" + "-".join(map(str, gene.location)) + "\n")
for i in xrange(0, len(proteins), 50):
output.write(proteins[i:min(i+50, len(proteins))] + "\n")
output.close()
self.panel.frame.blastLocation.background = Color.white
self.panel.frame.databaseLocation.background = Color.white
try:
utils.cachedBlast("profelis.query.blastp.xml", self.panel.frame.blastLocation.text, self.panel.frame.databaseLocation.text + "/" + self.panel.database, self.panel.evalue, "profelis.query.fas", self.panel, True)
except OSError:
self.panel.frame.blastLocation.background = Color.red
self.panel.frame.databaseLocation.background = Color.red
return
genes = utils.parseBlast("profelis.query.blastp.xml")[2]
self.panel.outGenes.model.clear()
[self.panel.inGenes.model.add(0, gene) for gene in genes[::-1]]
xml.addGenes(self.panel.name + ".blastp.xml", "profelis.query.blastp.xml")
xml.writeHTML(self.panel.name + ".blastp.xml")
self.panel.writeArtemisFile()
def actionPerformed(self, event):
output = open("profelis.query.fas", "w")
for gene in self.panel.outGenes.model.elements():
print gene.location
if gene.location[0] < gene.location[1]:
proteins = utils.translate(
self.panel.genome[gene.location[0] - 1:gene.location[1]])
else:
proteins = utils.translate(
utils.reverseComplement(
self.panel.genome[gene.location[1] -
1:gene.location[0]]))
output.write(">profelis" + ":" +
"-".join(map(str, gene.location)) + "\n")
for i in xrange(0, len(proteins), 50):
output.write(proteins[i:min(i + 50, len(proteins))] + "\n")
output.close()
self.panel.frame.blastLocation.background = Color.white
self.panel.frame.databaseLocation.background = Color.white
try:
utils.cachedBlast(
"profelis.query.blastp.xml",
self.panel.frame.blastLocation.text,
self.panel.frame.databaseLocation.text + "/" +
self.panel.database, self.panel.evalue, "profelis.query.fas",
self.panel, True)
except OSError:
self.panel.frame.blastLocation.background = Color.red
self.panel.frame.databaseLocation.background = Color.red
return
genes = utils.parseBlast("profelis.query.blastp.xml")[2]
self.panel.outGenes.model.clear()
[self.panel.inGenes.model.add(0, gene) for gene in genes[::-1]]
xml.addGenes(self.panel.name + ".blastp.xml",
"profelis.query.blastp.xml")
xml.writeHTML(self.panel.name + ".blastp.xml")
self.panel.writeArtemisFile()
def loadFile(self):
self.inGenes.model.clear()
self.database, self.evalue, genes = utils.parseBlast(self.name + ".blastp.xml")
[self.inGenes.model.addElement(gene) for gene in genes]
artemisInput = open(self.name + ".art", "r")
lines = artemisInput.readlines()
artemisInput.close()
self.restOfFile = self.genome = []
while lines:
if re.match("\s+CDS\s+(complement\()?\d+\.\.\d+\)?\n", lines[0]):
lines = lines[4:]
elif lines[0].find("ORIGIN") == 0:
self.genome = map(lambda x: re.sub("\s+", "", x), lines[1:])
lines = []
else:
if lines[0].strip():
self.restOfFile.append(lines[0])
lines = lines[1:]
self.genome = "".join(self.genome)
self.restOfFile = "".join(self.restOfFile)
def loadFile(self):
self.inGenes.model.clear()
self.database, self.evalue, genes = utils.parseBlast(self.name +
".blastp.xml")
[self.inGenes.model.addElement(gene) for gene in genes]
artemisInput = open(self.name + ".art", "r")
lines = artemisInput.readlines()
artemisInput.close()
self.restOfFile = self.genome = []
while lines:
if re.match("\s+CDS\s+(complement\()?\d+\.\.\d+\)?\n", lines[0]):
lines = lines[4:]
elif lines[0].find("ORIGIN") == 0:
self.genome = map(lambda x: re.sub("\s+", "", x), lines[1:])
lines = []
else:
if lines[0].strip():
self.restOfFile.append(lines[0])
lines = lines[1:]
self.genome = "".join(self.genome)
self.restOfFile = "".join(self.restOfFile)
