Preparing NGLess 1.3

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Luis Pedro Coelho

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Jan 20, 2021, 12:20:44 AM1/20/21
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Hi everyone,

I think we could do NGLess 1.3 soon. Like for 1.2, there haven't been any big "killer features" changes, but a bunch of small improvements (maybe most notably, read_int() and read_double() functions + to_string() methods).

If there are any small things that you think could be done, now is a good time to ask for them.

Best
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org
https://orcid.org/0000-0002-9280-7885

Vadim Puller

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Jan 22, 2021, 3:55:46 AM1/22/21
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Hi Luis,

A minor suggestion: including feature length  in the count table.
In a bit more details: `count` function may output the results normalized by the feature lengths: `{raw/normed/scaled}`. From the point of view of the downstream data manipulation, I would prefer to have raw reads that I could normalize by the feature length when necessary. As of now I have to import these lengths from the catalogue and merge them with the count table outside of NGLess.

A less minor disadvantage is the necessity to launch NGLess as many times as there are the samples. Thus, one has to use an external script or a different software for organizing workflow, reducing NGLess to a command line tool. But I suppose this is not counted as "small improvements"

Regards, Vadim.

Ulrike Löber

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Jan 22, 2021, 4:01:07 AM1/22/21
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Dear Luis,
I agree with Vadim regarding the parallel feature.
Could it be that the syntax for different catalogues differ? e.g. KEGG_KOs for IGC, KEGG_ko for GMGC? Could this be harmonized by setting aliasses at least for "built in" modules?

Best,
Ulrike
Am Freitag, 22. Januar 2021, 09:55:48 MEZ hat Vadim Puller <vpu...@gmail.com> Folgendes geschrieben:


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Luis Pedro Coelho

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Jan 22, 2021, 4:44:32 AM1/22/21
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1. I actually agree also that the parallel module's API is suboptimal. Maybe this is something that we improve for 1.4, so that there is a longer test period, though. I think a real solution may have to wait a bit longer still, but one simple improvement would be for NGLess to restart itself every time it is not done (this would be more similar to how Jug works, which was the original inspiration for this way of working).

2. We are implicitly becoming more consistent as we use eggnog-mapper2 for everything, but I agree that it has been done a bit haphazardly before.

HTH,
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org


Ulrike Löber

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Jan 22, 2021, 4:49:51 AM1/22/21
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Dear Luis,
This might be even an issue which somehow affects --validate-only which does not check the feature headers of the mapping files I guess? 
Results in positive scrip validation and abort process due to invalid syntax.
Best,
Ulrike


Am Fr., Jan. 22, 2021 at 10:44 schrieb Luis Pedro Coelho

Luis Pedro Coelho

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Jan 25, 2021, 5:37:24 AM1/25/21
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Oh, this is a very good point. The checks for headers are indeed not run on --validate-only (although they are run at the start of execution).

This does qualify as a simple enough fix that I can still make it for 1.3. It's just a matter of reorganizing the existing, code.

Tx
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org


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