def importgff(self, myfile):
"""imports a gff file and creats an internal object"""
f = file(myfile, 'r')
gfflist = FeatureList("gff")
genomedataTemp = f.readlines()
genomedataTemp = genomedataTemp[5:]
genomedataTemp = genomedataTemp[:len(genomedataTemp) -1]
# Split lines of file
for eachline in genomedataTemp:
eachline = eachline.strip()
tmpl = eachline.split('\t')
feature = Feature(tmpl[2], tmpl[8], int(tmpl[3]), int(tmpl[4]))
gfflist.addFeature(feature)
f.close()
con.addGFFList(gfflist)
def regexsearch(self, patterns):
"""search in a string with a re"""
genome = Imports.genome
regex = re.compile(patterns)
matches = regex.finditer(genome.getSequence())
regexlist = FeatureList("Search for: " + patterns)
if patterns != "":
for match in matches:
feature = Feature("RegEx-Result at: " + str(match.start()),"Gene Sequence", match.start(),match.end() )
regexlist.addFeature(feature)
if regexlist.getLength()> 1:
wx.MessageBox(str(regexlist.getLength())+" matches found!", style=wx.OK)
Imports.con.addFeatureList(regexlist)
Imports.con.setChanged()
#TreeView.AddTreeNodes(self.treeview.searchResults, matches)
else: wx.MessageBox("No matches found!", style=wx.OK)
else: wx.MessageBox("Please enter a regular expression!", style=wx.OK)
def importptt(self, myfile):
"""imports a ptt file and creates and internal object"""
f = file(myfile, 'r')
self.name = f.readline()
self.proteins = f.readline()
pttlist = FeatureList("ptt")
genomedataTemp = f.readlines()
genomedataTemp = genomedataTemp[1:]
for eachline in genomedataTemp:
eachline = eachline.strip()
tmpl = eachline.split('\t')
l = tmpl[0].split("..")
tmpl = tmpl[1:]
tmpl = l+tmpl
feature = Feature(tmpl[9],tmpl[9],int(tmpl[0]), int(tmpl[1]))
pttlist.addFeature(feature)
f.close()
con.addPTTList(pttlist)
def importgff(self, myfile):
"""imports a gff file and creats an internal object"""
f = file(myfile, 'r')
if myfile.endswith('.gff'):
gfflist = FeatureList("gff")
genomedataTemp = f.readlines()
genomedataTemp = genomedataTemp[5:]
genomedataTemp = genomedataTemp[:len(genomedataTemp) -1]
# Split lines of file
for eachline in genomedataTemp:
eachline = eachline.strip()
tmpl = eachline.split('\t')
feature = Feature(tmpl[2], tmpl[8], int(tmpl[3]), int(tmpl[4]))
gfflist.addFeature(feature)
f.close()
con.addGFFList(gfflist)
else:
wx.MessageBox("No GFF-File given, pleasy try again","Fatal Import Error", style=wx.OK)
f.close()
def __init__(self, parent, id, title):
wx.Frame.__init__(self, parent, id, title, size=(800, 400))
genome = Genome()
genome.setSequence("")
featurelist = FeatureList("test")
feature1 = Feature("protein1", "protein asdgqiuw", 0, 49)
feature2 = Feature("protein2", "asdgqidu", 270, 300)
featurelist.addFeature(feature1)
featurelist.addFeature(feature2)
gff = FeatureList("gff")
featuregff1 = Feature("protein1", "protein asdgqiuw", 60, 70)
featuregff2 = Feature("protein1", "protein asdgqiuw", 78, 80)
gff.addFeature(featuregff1)
gff.addFeature(featuregff2)
flc = FeatureListContainer()
flc.addFeatureList(featurelist)
flc.addFeatureList(gff)
self.model = GenomeModel()
self.model.setGenome(genome)
self.model.setFeatureListContainer(flc)
self.view = GenomeView(self.model, self)
self.Show()
def importptt(self, myfile):
"""imports a ptt file and creates and internal object"""
f = file(myfile, 'r')
if myfile.endswith('.ptt'):
self.name = f.readline()
self.proteins = f.readline()
pttlist = FeatureList("ptt")
genomedataTemp = f.readlines()
genomedataTemp = genomedataTemp[1:]
for eachline in genomedataTemp:
eachline = eachline.strip()
tmpl = eachline.split('\t')
l = tmpl[0].split("..")
tmpl = tmpl[1:]
tmpl = l+tmpl
feature = Feature(tmpl[9],tmpl[9],int(tmpl[0]), int(tmpl[1]))
pttlist.addFeature(feature)
f.close()
con.addPTTList(pttlist)
else:
wx.MessageBox("No PTT-File given, pleasy try again","Fatal Import Error", style=wx.OK)
f.close()
