lpantano on v0.4.22
lpantano on master
fix edge case where limit==vari… Merge branch 'dev' of github.co… bump version and 5 more (compare)
lpantano on dev
hot fix Merge branch 'master' into dev (compare)
lpantano on dev
bump to 22 (compare)
good first issuelabel
gff2sqlso we can re use it for query beside db creation
automaticis for testing command lines (https://github.com/miRTop/mirtop/blob/master/test/test_automated_analysis.py#L348), and the
functionis to test functions (https://github.com/miRTop/mirtop/blob/master/test/test_functions.py#L168).
@lpantano , Hi. I have completed: (a) integrate the script in the mirtop code (with mirtop convert --format sql ); (b) add test units.
I was able to test the test_functions.py with
-m unittest run and there was no error;
while due to two versions of python (2 and 3) and mirtop installed in my computer, I am not able to test through test_automated_analysis.py. However, with complete path outside the test run I am able to run the code successfully.
Is there any other way of testing the function?
Also, for other functions there were some files missing for example (No such file or directory: 'razers3': 'razers3': for spikein_cmd) and for few path were incorrect (../data/example)
Sure, thank you. Yes
nosetests ran without errors, I used
-m unittest. This fixed the path issues, except for missing razers file for spikein_cmd. I am having only this following error:
subprocess.CalledProcessError: Command '['mirtop', 'convert', '--format', 'sql', '-o', 'test_out_mirs', '--db', 'test_sqlite.db', '--gff', '../../data/examples/gff/correct_file.gff']' returned non-zero exit status 2.
However, it is successful if I run it this way:
/home/csbmm/miniconda2/bin/mirtop convert --format sql -o test_out_mirs --db test_sqlite.db --gff correct_file.gff
['convert', '--format', 'sql', '-o', 'test_out_mirs', '--db', 'test_sqlite.db', '--gff', 'correct_file.gff']
09/14/2019 03:22:26 INFO Run Convert GFF.
09/14/2019 03:22:26 INFO It took 0.002 minutes
mirtop convert --format queryfunction for future use.