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Have Mikado serialise scoop the junction coordinates from the block_size/block_starts #382

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lucventurini opened this issue Feb 26, 2021 · 0 comments · Fixed by #383
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Have Mikado serialise scoop the junction coordinates from the block_size/block_starts #382

lucventurini opened this issue Feb 26, 2021 · 0 comments · Fixed by #383
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@ljyanesm
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enhancement
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2.1.2

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@lucventurini
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Currently mikado serialise uses the thick_start, thick_end coordinates to impute the position of the junction.
However, this is incompatible with e.g. TopHat junctions or user-provided junctions.

@ljyanesm suggested using instead the block starts and sizes to impute those positions. This should be more portable.
@lucventurini lucventurini added this to the 2.1.2 milestone Feb 26, 2021
@lucventurini lucventurini mentioned this issue Feb 26, 2021
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lucventurini added a commit that referenced this issue Mar 15, 2021
@lucventurini
Fix v2.1.2 (#383)
469b1c7 
# Version 2.2.0
Removed Cython from the requirements.txt file. This allows to perform the tests correctly in a Conda environment (as Conda disallows installing Cython as part of a distributed package).
As a result of this change, the preferred installation procedure from source has to be slightly amended:
- either install using `pip wheel -w dist . && pip install dist/Mikado*whl`
- or install with `python setup.py bdist_wheel` **after** having forcibly installed Cython, with `pip install Cython` or the like.

Other changes:
- Fix [#381](#381): now Mikado will be able to guess correctly 
  the input file format, instead of relying on the file name extension or user's settings. Sniffing for files 
  provided as a stream is *disabled* though.
- Fix [#382](#382): now Mikado can accept generic BED12 files 
  as input junctions, not just Portcullis junctions. This allows e.g. a user to provide a ***set of gene models*** 
  in BED12 format as sources of valid junctions.
- Fix [#384](#384): now Mikado convert deals properly with 
  unsorted GTFs/GFFs. 
- Fix [#386](#386): dealing better with unsorted GFFs/GTFs for 
  the stats utility.
- Fix [#387](#387): now Mikado will always use a static seed, 
  rather than generating a new one per call unless specifically instructed to do so. The old behaviour can still be 
  replicated by either setting the `seed` parameter to `null` (ie `None`) in the configuration file, or by 
  specifying `--random-seed` during the command invocation.
- General increase in code unit-test coverage; in particular:  
  - Slightly increased the unit-test coverage for the locus classes, e.g. properly covering the `as_dict` and `load_dict`
    methods. Minor bugfixes related to the introduction of these unit-tests.
- `Mikado.parsers.to_gff` has been renamed to `Mikado.parsers.parser_factory`.
- The code related to the transcript padding has been moved to the submodule `Mikado.transcripts.pad`, rather than 
  being part of the `Mikado.loci.locus` submodule.
- Mikado will error informatively if the scoring configuration file is malformed.
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Fix v2.1.2 EI-CoreBioinformatics/mikado
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@ljyanesm @lucventurini