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()