User: adrian.altenhoff
adrian.altenhoff • 620
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Posts by adrian.altenhoff
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... Maybe important to mention that for this exact application of downloading for one or more whole genomes a fasta file of protein sequences, it is much more efficient to use the download link for all protein sequences in fasta format and filter for the genomes of interest. The URL for the latest versi ...
written 5 weeks ago by
adrian.altenhoff • 620
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... Dear Sally,
the difference is the expected behaviour. Note that in the Map-SeqNum-ID.txt file, the numeric column (8460 in your example) starts from 1 for every genome. So the 8460 is not a unique ID. The id attribute in the tag of the orthoxml file however must be unique.
About your question to ...
written 6 weeks ago by
adrian.altenhoff • 620
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... Dear Hannah,
there is not a way to directly load whole genomes in fasta format using the PyOMADB tool. However, you can load multiple proteins at once:
import omadb
c = omadb.Client()
ids = ["HUMAN{:05d}".format(x) for x in range(1, 55)]
c.proteins.info(ids)
Note that the number ...
written 6 weeks ago by
adrian.altenhoff • 620
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... Hi Nicki,
yes, for genomes that do not have splicing information, all the protein sequences are treated as independable genes and are most likely inferred as paralogs. One reason why they might not is due to very different lengths, in which case OMA might decide not to call them as orthologs/paralo ...
written 6 weeks ago by
adrian.altenhoff • 620
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... Hi,
currently pyham does not have an option to skip some gene elements from an orthoxml file. But we agree that this is an important feature and plan to implement it in the future.
As a short term fix, the easiest option in my view is to remove in the orthoxml file the elements that do not corre ...
written 6 weeks ago by
adrian.altenhoff • 620
2
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... Dear Marton,
generally speaking, the weblink on the genome page should direct you to the page from where we downloaded originally the genome.
Many of the older bacteria - including your Salmonella strain - come originally from Expasy's `GenomeReviews` - a service that is no longer maintained. The ...
written 6 weeks ago by
adrian.altenhoff • 620
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... Hi Nicki,
1) it's good that the find command did not returned any result (that means there was no pending checkpoint file).
2) which version of OMA standalone are you using? could it be the same issue than https://www.biostars.org/p/365017/ ? That should be fixed in OMA standalone 2.3.1
3) that i ...
written 9 weeks ago by
adrian.altenhoff • 620
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... Hi Sally,
what you see here happens indeed much later than loading the AllAll
files, so it was indeed a buffering problem. You should indeed increase
the walltime limit to something bigger and your computation will
hopefully nicely run through.
Best wishes
Adrian
...
written 9 weeks ago by
adrian.altenhoff • 620
0
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... Hi Nicki, that is indeed quite weird. Did you try starting OMA again. It should anyways generate the missing part files then, without redoing anything that has previously been computed.
Could you also check if you have any checkpoint files in the AllAll directory:
`find Cache/AllAll -type f -name ...
written 9 weeks ago by
adrian.altenhoff • 620
2
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... Hi Sally,
I'm one of the developers of OMA standalone. Couldn't it be just a buffering issue of the stdout and stderr streams? Certain HPC clusters keep a large buffer before data is written to disk, and during the phase of reading these files we don't produce a lot of output... Once the process ge ...
written 9 weeks ago by
adrian.altenhoff • 620
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6 weeks ago,
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For A: OMA error in stage 2 of 2 stage process
Scholar
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For A: OMA error in stage 2 of 2 stage process
Scholar
17 months ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
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2.2 years ago,
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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3.1 years ago,
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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For A: Is this warning fatal in OMA
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3.3 years ago,
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For A: Is this warning fatal in OMA
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3.3 years ago,
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For A: Is this warning fatal in OMA
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For A: Gene Gain/loss + Duplication Tree
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For A: Gene Gain/loss + Duplication Tree
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For A: What exactly is OMA doing here ?
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3.5 years ago,
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For A: Gene Gain/loss + Duplication Tree
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