Mikado prepare freezes if one of the input files has the wrong extension #381
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lucventurini
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lucventurini
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…s impossible without digging really deeply into how Python deals with pipes and streams, so we will shelve it for now.
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lucventurini
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# 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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To reproduce:
#. Go into
sample_data#. Change
trinity.gff3totrinity.gtfin thelist.txtfile#. launch
snakemake daijin.Mikado prepare will emit an error (showing that one of the child processes died due to not being able to parse the input properly) and then hang indefinitely.
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