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doRiNa - database of posttranscriptional regulatory elements

License: GNU General Public License v3.0

Makefile 0.10% Python 43.72% Scheme 0.88% Shell 1.47% HTML 0.35% Jupyter Notebook 53.48%
bioinformatics database genome pybedtools python regulatory-network

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dorina's Issues

Python 3.6 support

Python 3.6 is the latest stable version of Python programming language. It's more secure and generally faster than Python 2.7.
This issue aims to refactor dorina and webdorina code for py36 without dropping py27 support.

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 510: ordinal not in range(128)

Upon starting apache2 on carina-dev, and attempting to access the website, access failed with an error (in /var/log/apache2/error.log) as follows:

Fri Jan 19 13:48:04.425583 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512] mod_wsgi (pid=25443): Target WSGI script '/home/carina/webdorina/webdorina/webdorina.wsgi' cannot be loaded as Python module.
[Fri Jan 19 13:48:04.425711 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512] mod_wsgi (pid=25443): Exception occurred processing WSGI script '/home/carina/webdorina/webdorina/webdorina.wsgi'.
[Fri Jan 19 13:48:04.425785 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512] Traceback (most recent call last):
[Fri Jan 19 13:48:04.426417 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/home/carina/webdorina/webdorina/webdorina.wsgi", line 16, in <module>
[Fri Jan 19 13:48:04.426475 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     from webdorina.app import app as application
[Fri Jan 19 13:48:04.426937 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/home/carina/webdorina/webdorina/app.py", line 41, in <module>
[Fri Jan 19 13:48:04.426997 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     Regulator.init(app.config['DATA_PATH'])
[Fri Jan 19 13:48:04.427659 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/usr/local/lib/python3.4/dist-packages/dorina/regulator.py", line 65, in init
[Fri Jan 19 13:48:04.427722 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     parse_func)
[Fri Jan 19 13:48:04.427957 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/usr/local/lib/python3.4/dist-packages/dorina/utils.py", line 33, in walk_assembly_tree
[Fri Jan 19 13:48:04.428087 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     species_dict[assembly] = parse_func(assembly_path)
[Fri Jan 19 13:48:04.428151 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/usr/local/lib/python3.4/dist-packages/dorina/regulator.py", line 55, in parse_func
[Fri Jan 19 13:48:04.428304 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     experiments = parse_experiment(experiment_path)
[Fri Jan 19 13:48:04.428372 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/usr/local/lib/python3.4/dist-packages/dorina/regulator.py", line 32, in parse_experiment
[Fri Jan 19 13:48:04.428718 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     return json.load(fh)
[Fri Jan 19 13:48:04.429431 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/usr/lib/python3.4/json/__init__.py", line 265, in load
[Fri Jan 19 13:48:04.429514 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     return loads(fp.read(),
[Fri Jan 19 13:48:04.429729 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]   File "/usr/lib/python3.4/encodings/ascii.py", line 26, in decode
[Fri Jan 19 13:48:04.429855 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512]     return codecs.ascii_decode(input, self.errors)[0]
[Fri Jan 19 13:48:04.429918 2018] [wsgi:error] [pid 25443:tid 140426388211456] [remote 129.206.148.116:512] UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 510: ordinal not in range(128)

Pypy support

Pypy is an alternative for Just In Time compilation of Python code - that does not require any changes in pure Python code to work. Cython and C extension may require work.

I anticipate that Pybeedtools is not Pypy compatible but I will look into this issue further. Also, Pypy does not support Pandas and Numpy support is rather limited.

Cross-species comparisons

Cross-species comparison is a relevant feature to the study of cardiovascular diseases. Carina should support:

  • Gene trees
  • RNA-RNA alignments Visualization

Support for new data types

Add support for the following types of data:

  • Polymorphism
  • Gene Expression
  • ENCODE eCLIP and Bind-n-seq data
  • Ribo-Seq
  • Proteomics

Centralised logging

Both Dorina and webdorina lack a centralised logging system and the code is debugged with print statements.

Data update

Carina next milestone shifts the database focus on regulatory elements and RNA interaction in the Cardiac system and cardiovascular disease.

The shift will include literature systematic review for new data sets. Due to a large number of data sets and scientific articles on Cardiology, a semi-automated curation is recommended. The tool should first sift thought papers and databases for potential targets, which should be human curated.

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