Cannot compute TSSes or TESes without strand info

[EmilVorsteveld]

Using GTF files from GENCODE, I get the following error:

cerberus gtf_to_bed --gtf gencode.v45.annotation.gtf -o gencode.v45.annotation.out --mode tss

Exception: Cannot compute TSSes or TESes without strand info. Perhaps use extend() or subsequence() or spliced_subsequence() instead?

[fairliereese]

Without digging into the issue too much, I have a feeling this might be caused by strange PyRanges stranded vs. unstranded behavior that I've been encountering lately (see this issue). Either way, I recommend installing my version of PyRanges for use with Cerberus. Try this and let me know if it solves your issue!

[EmilVorsteveld]

This indeed solves this issue, thanks.
Unfortunately, for me, the agg_ics function throws the following error:
File "/Users/emilvorsteveld/miniforge3/envs/cerberus/lib/python3.9/site-packages/pandas/core/internals/base.py", line 57, in _validate_set_axis
raise ValueError(
ValueError: Length mismatch: Expected axis has 4 elements, new values have 3 elements

I have tried older pandas versions (1.3.0 and 1.5.3), but not luck...

[fairliereese]

Hi, sorry for the delay. Can you please attach the complete error message stack trace so I can see what line in Cerberus threw the error?

Thanks!

[Yuej24]

Hi, I also met the same problem (ValueError: Length mismatch: Expected axis has 4 elements, new values have 3 elements). Here is my complete error message trace:
Traceback (most recent call last):
File "/usr/local/bin/cerberus", line 8, in
sys.exit(cli())
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/cerberus/main.py", line 71, in agg_ics_command
return agg_ics_config(input, o)
File "/usr/local/lib/python3.8/site-packages/cerberus/cerberus.py", line 2272, in agg_ics_con
fig
ics, refs, sources = parse_agg_ics_config(input)
File "/usr/local/lib/python3.8/site-packages/cerberus/cerberus.py", line 1713, in parse_agg_i
cs_config
df.columns = ['fname', 'ref', 'source']
File "/usr/local/lib/python3.8/site-packages/pandas/core/generic.py", line 6002, in __setattr
__
return object.setattr(self, name, value)
File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.set
File "/usr/local/lib/python3.8/site-packages/pandas/core/generic.py", line 730, in _set_axis
self._mgr.set_axis(axis, labels)
File "/usr/local/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 225, in
set_axis
self._validate_set_axis(axis, new_labels)
File "/usr/local/lib/python3.8/site-packages/pandas/core/internals/base.py", line 70, in _validate_set_axis
raise ValueError(
ValueError: Length mismatch: Expected axis has 4 elements, new values have 3 elements