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feature: attemping translation with diamond and BlastX #88

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feature: attemping translation with diamond and BlastX #88

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gordonkoehn
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Doing the translation with Diamond and BlastX.

gordonkoehn and others added 3 commits January 30, 2025 13:57
@gordonkoehn @Copilot
[fix]: Docs - adding missing dependency (#85)
d529b1e 
* fix missing dependency

* Update pyproject.toml

Co-authored-by: Copilot <[email protected]>

* dep cobflixt

---------

Co-authored-by: Gordon J. Köhn <[email protected]>
Co-authored-by: Copilot <[email protected]>
enhance docstring
f3fa819
makeeing a start with blastX
df13810
@gordonkoehn gordonkoehn mentioned this pull request Jan 30, 2025
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@gordonkoehn gordonkoehn linked an issue Jan 30, 2025 that may be closed by this pull request
Translate & Align V-Pipe Reads #53
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Alright - so there is a new issue.

The current function bam_to_fastq_with_indels handles adds "-" in sequences for deletions.

This is not a common fastq format. I don't know what is?

I should also not do this function myself, rather use pysam and kick out insertions.

https://gemini.google.com/app/302a01c54e6fe493

Note that at a later stage I may want to add insertions with "_" again to the sequence.

@gordonkoehn gordonkoehn self-assigned this Feb 7, 2025
@gordonkoehn gordonkoehn added enhancement New feature or request python Pull requests that update Python code labels Feb 7, 2025
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Translate & Align V-Pipe Reads
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