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  • Sep 18 19:19
    lpantano commented #59
  • Sep 14 11:05
    codecov[bot] commented #59
  • Sep 14 11:03
    codecov[bot] commented #59
  • Sep 14 11:00
    arunhpatil synchronize #59
  • Sep 14 10:33
    arunhpatil opened #59
  • Sep 13 22:22
    codecov[bot] commented #58
  • Sep 13 22:22

    lpantano on v0.4.22

    (compare)

  • Sep 13 22:22
    codecov[bot] commented #58
  • Sep 13 22:21

    lpantano on master

    fix edge case where limit==vari… Merge branch 'dev' of github.co… bump version and 5 more (compare)

  • Sep 13 22:21
    lpantano closed #58
  • Sep 13 22:20
    codecov[bot] commented #58
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    codecov[bot] commented #58
  • Sep 13 22:17
    lpantano synchronize #58
  • Sep 13 22:17

    lpantano on dev

    hot fix Merge branch 'master' into dev (compare)

  • Sep 13 22:12
    codecov[bot] commented #58
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    codecov[bot] commented #58
  • Sep 13 22:07
    lpantano opened #58
  • Sep 13 22:07

    lpantano on dev

    bump to 22 (compare)

  • Sep 05 13:32
    lpantano commented #57
  • Sep 05 11:19
    illumination-k edited #57
Lorena Pantano
@lpantano
new issues for people who wants to start contributing: https://github.com/miRTop/mirtop/issues. Look for good first issue label
Lorena Pantano
@lpantano
Hi all, please feel free to distribute this: looking for a logo: miRTop/mirtop#29
Lorena Pantano
@lpantano
well, here we start the cofest day!
miRTop/mirtop#13, for @vbarrera
another one that could be good to have if you want to play with multiqc is miRTop/mirtop#33
this is good for newcomers, to try to catch more tools: miRTop/mirtop#11
Lorena Pantano
@lpantano
to read lines from GFF we have a function: https://github.com/miRTop/mirtop/blob/dev/mirtop/gff/body.py#L144
Kieran O'Neill
@oneillkza
Support for mirtop is currently in a pull request to MultiQC: ewels/MultiQC#788
This includes a summary table now!
Lorena Pantano
@lpantano
thanks!
Lorena Pantano
@lpantano
hey all, we’ll work on the tool during this online hackathon organized by brad chapman: online CoFest next Friday, August 17; everyone is welcome to join: https://www.open-bio.org/wiki/CoFest_2018_August
Arun Patil
@arunhpatil
@lpantano , Hi. This is regarding miRTop/mirtop#56 . I have written function 'gff2sql' and is available at https://github.com/arunhpatil/mirtop/tree/master/mirtop/gff2sql, Kindly let me know if this is fine?
Arun Patil
@arunhpatil
Instead of having 'mirtop convert --format sql' I have it as 'mirtop gff2sql' which can be used to 'create or query' the database? is this fine or should it be 'convert --format sql'?
Also, although I could edit the command_line.py script locally, I am unable to locate and append the option in mirtop script.
how do I add test units?
Lorena Pantano
@lpantano
Thank you @arunhpatil
You can add the subcommand in the file lib/parse.py, you will need to add another subcommand, I would say sql instrad of gff2sql so we can re use it for query beside db creation
for the unit test, you can add the functions in the tests/*py files. the automatic is for testing command lines (https://github.com/miRTop/mirtop/blob/master/test/test_automated_analysis.py#L348), and the function is to test functions (https://github.com/miRTop/mirtop/blob/master/test/test_functions.py#L168).
Arun Patil
@arunhpatil
Great, got it. I will edit the code accordingly and update . Thanks @lpantano.
Arun Patil
@arunhpatil

@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)

Arun Patil
@arunhpatil
Please find the link for the repository https://github.com/arunhpatil/mirtop
Lorena Pantano
@lpantano
Thanks. I will take a look on Monday, aboute the paths for the tests…it is weird, travis passess without error, you need to run it inside the mirtop folder as: nosetests, that will run all.
And I am keeping just python 3, and droping python 2.7 since everybody is moving away from that.
Arun Patil
@arunhpatil

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:
$ python3.7 /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

Arun Patil
@arunhpatil
image.png
It worked with Travis with 81% coverage and I have also included mirtop convert --format query function for future use.
Lorena Pantano
@lpantano
thank you, this is getting great.
Arun Patil
@arunhpatil
Thanks
Lorena Pantano
@lpantano
Arun, here is the big GFF file with 300-400 samples: https://www.dropbox.com/s/7yg09jnw8xv1n95/mirtop.tar.gz?dl=1