User: adrian.altenhoff
adrian.altenhoff • 620
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Posts by adrian.altenhoff
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... Hi Biojl,
I've fixed the problem, please upgrade to pyham >= 1.1.7 e.g.
pip install --upgrade pyham ...
written 5 months ago by
adrian.altenhoff • 620
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... Hi Biojl
indeed, that seems to be a bug in the pyham library. will fix it asap and release a fixed version on pypi. Thanks for reporting.
Adrian ...
written 5 months ago by
adrian.altenhoff • 620
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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 7 months 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 7 months 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 7 months 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 7 months ago by
adrian.altenhoff • 620
2
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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 7 months 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 7 months 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 8 months 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 8 months ago by
adrian.altenhoff • 620
Latest awards to adrian.altenhoff
Scholar
7 months ago,
created an answer that has been accepted.
For A: OMA error in stage 2 of 2 stage process
Scholar
8 months ago,
created an answer that has been accepted.
For A: OMA error in stage 2 of 2 stage process
Scholar
23 months ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
Scholar
3.2 years ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
Scholar
3.5 years ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
Teacher
3.6 years ago,
created an answer with at least 3 up-votes.
For A: Is this warning fatal in OMA
Scholar
3.6 years ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
Scholar
3.8 years ago,
created an answer that has been accepted.
For A: Is this warning fatal in OMA
Teacher
3.8 years ago,
created an answer with at least 3 up-votes.
For A: Is this warning fatal in OMA
Scholar
3.9 years ago,
created an answer that has been accepted.
For A: Gene Gain/loss + Duplication Tree
Scholar
4.0 years ago,
created an answer that has been accepted.
For A: Gene Gain/loss + Duplication Tree
Teacher
4.0 years ago,
created an answer with at least 3 up-votes.
For A: What exactly is OMA doing here ?
Scholar
4.0 years ago,
created an answer that has been accepted.
For A: Gene Gain/loss + Duplication Tree
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