Mercurial > repos > cschu > candisnp
diff candisnp.py @ 5:9215ffe7d4d5 draft
Fixed issue with INDEL annotations. Changed output to iframe.
| author | cschu |
|---|---|
| date | Wed, 24 Jun 2015 11:42:40 -0400 |
| parents | 36f6520671b3 |
| children |
line wrap: on
line diff
--- a/candisnp.py Fri May 22 13:38:13 2015 -0400 +++ b/candisnp.py Wed Jun 24 11:42:40 2015 -0400 @@ -119,7 +119,8 @@ 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(';')) + 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')) @@ -199,9 +200,12 @@ 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) + # 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)