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Not for ENA submission: Sequence too short #78

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CEPHAS-01 opened this issue Aug 8, 2023 · 0 comments · Fixed by #80
Closed

Not for ENA submission: Sequence too short #78

CEPHAS-01 opened this issue Aug 8, 2023 · 0 comments · Fixed by #80

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@CEPHAS-01
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Is your feature request related to a problem? Please describe.

I am not submitting the sequences to ENA, but to create a repeats library to be concatenated with RepeatMasker library. I need to have all the repeats model represented, so 100bp cannot be a limit that is acceptable.

Describe the solution you'd like
Ability to convert sequences less than 100bp to the EMBL format. I do not want to pad the sequence with Ns, it wouldn't make any sense.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Representation of repeats models where the sequences could be less than 100bp.
Juke34 added a commit that referenced this issue Sep 1, 2023
@Juke34
add parameter to keep short sequences (< 100bp) --keep_short_sequences.
1bf6990 
Fix #78
@Juke34 Juke34 mentioned this issue Sep 1, 2023
Merged
@Juke34 Juke34 closed this as completed in #80 Sep 1, 2023
Juke34 added a commit that referenced this issue Sep 1, 2023
@Juke34
Merge pull request #80 from NBISweden/2.3.0
d7a7f35 
* Remove python_version>="3.8.0" from install_requires section in setup.py that was not working properly. Use instead old fashion test e.g. if sys.version_info < (3,9): sys.exit('Sorry, Python >= 3.9 is required')
This change fix Installation issue EMBLmyGFF3 & python version requirements #79 , fix if I can specify certain python source during python setup.py install #77
* Update test : Remove dates for comparison between expected output and result (DT and RL lines). Change taxonomy for prokka test that has recently changed in NCBI taxonomy DB.
* Move minimum python requirement from python 3.8 to python 3.9 due to solve some dependencies requirement issues
* fix Not for ENA submission: Sequence too short #78 add possibility to avoid to skip short sequences (< 100 nt)
* Change badge in Readme for CI
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2.2.1 NBISweden/EMBLmyGFF3
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@CEPHAS-01