extract_intervals- AttributeError: 'NoneType' object has no attribute 'group' with GENCODE gtf

Using extract_intervals on a GENCODE gtf file like these resulted in this error:

ubuntu@olgabot-loom:~$ velocyto extract_intervals gencode.vM15.annotation.gtf -p gencode.vM15.annotation.velocyto-intervals.txt
2017-10-24 23:14:54,320 - DEBUG - Reading /home/ubuntu/gencode.vM15.annotation.gtf
Traceback (most recent call last):
  File "/home/ubuntu/anaconda/bin/velocyto", line 11, in <module>
    load_entry_point('velocyto==0.9.6', 'console_scripts', 'velocyto')()
  File "/home/ubuntu/anaconda/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/ubuntu/anaconda/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/ubuntu/anaconda/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/ubuntu/anaconda/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ubuntu/anaconda/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/ubuntu/anaconda/lib/python3.6/site-packages/velocyto/commands/extract_intervals.py", line 95, in extract_intervals
    exonno = regex_exonno.search(tags).group(1)
AttributeError: 'NoneType' object has no attribute 'group'
ubuntu@olgabot-loom:~$ which python
/home/ubuntu/anaconda/bin/python
ubuntu@olgabot-loom:~$ python --version
Python 3.6.2 :: Anaconda custom (64-bit)

[olgabot]

For anyone that finds this thread in the future, the ENSEMBL GTFs work.

[gioelelm]

I think the problem was less complex than we thought. It was related to one regular expression that anyway I was not using downstream. I removed it.

There is one extra problem left, when I process your gtf example above (but not other GENCODE gtfs). But I think it is only because your example is missing the transcript_name entry. I think that entry is mandatory http://www.gencodegenes.org/gencodeformat.html

So I consider fixed. Feel free to reopen the issue if you encounter further problems