comparison candisnp.py @ 5:9215ffe7d4d5 draft

Fixed issue with INDEL annotations. Changed output to iframe.

4:28990f586370

        self.position = int(args[1])
        self.reference_base = args[3]
        self.alternate_base = args[4]
     
        # info = dict([field.split('=') for field in args[7].strip().split(';')])
        info = dict(field.split('=') for field in args[7].strip().split(';'))
        # self.log.write('***'+str(info.get('EFF', '@@@')+'***\n'))
        
        self.allele_frequency = float(info.get('AF', '0.0'))
        self.effects = [effect 
                        for effect in info.get('EFF', '').split(',')

    except urllib2.URLError, e:
        candiURL = ''
        sys.stderr.write(str(e.reason) + '\n')
   
    if candiURL:
        body = urllib2.urlopen(candiURL)
        fo.write(body.read())
        #fo.write('<iframe src="%s"></iframe>\n' % candiURL)
    else:
        fo.write('I am sorry. CandiSNP does not pick up. Maybe (<a href="%s" target="_blank">try it manually?</a>)\n' % CANDISNP_SERVER)
     
    fo.close()
    pass

5:9215ffe7d4d5

        self.position = int(args[1])
        self.reference_base = args[3]
        self.alternate_base = args[4]
     
        # info = dict([field.split('=') for field in args[7].strip().split(';')])
        # info = dict(field.split('=') for field in args[7].strip().split(';'))
        info = dict(field.split('=') for field in args[7].strip().split(';') if len(field.split('=')) == 2)
        # self.log.write('***'+str(info.get('EFF', '@@@')+'***\n'))
        
        self.allele_frequency = float(info.get('AF', '0.0'))
        self.effects = [effect 
                        for effect in info.get('EFF', '').split(',')

    except urllib2.URLError, e:
        candiURL = ''
        sys.stderr.write(str(e.reason) + '\n')
   
    if candiURL:
        # body = urllib2.urlopen(candiURL)
        # fo.write(body.read())
        #fo.write('<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="%s"></iframe>' % candiURL)
        #fo.write('<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="%s"></iframe>' % candiURL)     
        fo.write('<iframe src="%s" frameborder="0" style="position: absolute; width: 100%%; height: 100%%;"></iframe>\n' % candiURL)
        # fo.write('<iframe src="%s"></iframe>\n' % candiURL)
    else:
        fo.write('I am sorry. CandiSNP does not pick up. Maybe (<a href="%s" target="_blank">try it manually?</a>)\n' % CANDISNP_SERVER)
     
    fo.close()
    pass