Example 1 problem

[nataliesilmon]

Hi, I am trying to follow example 1 for metaseq (https://daler.github.io/metaseq/example_session.html) and am having problems with the example data.

I'm following the script by copying from the example page (or the jupyter example page) - it will not generate an example.features file (though the example.npz file is generated). Can you please help me?

code:
metaseq.persistence.save_features_and_arrays(
features=tsses,
arrays={'ip': ip_array, 'input': input_array},
prefix='example',
link_features=True,
overwrite=True)

output:
ln: example.features: No such file or directory

[daler]

That function, when link_features=True (as in this example), will create a symlink rather than copy the data. What happens when you use link_features=False?

[nataliesilmon]

When I use link_features=False, I don't see the no such file or directory error, but still when I move on to the next section I get an error and can't proceed:

code:

features, arrays = metaseq.persistence.load_features_and_arrays(prefix='example')

output:
Traceback (most recent call last):
File "", line 1, in
File "/Users/Natalie/miniconda/envs/metaseq-test/lib/python2.7/site-packages/metaseq/persistence.py", line 24, in load_features_and_arrays
features = pybedtools.BedTool(prefix + '.features')
File "/Users/Natalie/miniconda/envs/metaseq-test/lib/python2.7/site-packages/pybedtools/bedtool.py", line 450, in init
raise ValueError('File "%s" does not exist' % fn)
ValueError: File "example.features" does not exist

[daler]

I'm unable to reproduce this. Things to check: Does tsses-1kb.gtf exist as created in the previous step(s)? How about tsses.gtf? Can you try restarting the session in a different directory? Are there any permission issues in the working directory?