User: george.ry
george.ry • 980
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Posts by george.ry
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1
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... This isn't your problem I don't think ... the package isn't handling it's own imports properly. You probably just need to change `from . import get_version` to `from GFFUtils import get_version`.
The program isn't doing anything particularly exciting anyway, though, so you could also just do it in ...
written 7 months ago by
george.ry • 980
3
votes
3
answers
1.1k
views
3
answers
... As per the link in the error message, SRA has moved from HTTP to HTTPS, rendering all previous versions of the SRA toolkit obsolete. You say you downloaded 2.8.1, but you still appear to be running 2.3.5, so I'd check what version is in your `$PATH` and where you installed the latest version. ...
written 7 months ago by
george.ry • 980
0
votes
1
answer
321
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1
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... Am I right in guessing that you're on a Mac, then?
// EDIT // Answering myself, the answer is that you are. OSX doesn't have GNU sed, so you'll need to install it with homebrew (etc). ...
written 8 months ago by
george.ry • 980
2
votes
1
answer
321
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1
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... New file: `sed '1~4s/\/1$//' myfile.fq > mynewfile.fq`
Inplace: `sed -i '1~4s/\/1$//' myfile.fq` ...
written 8 months ago by
george.ry • 980
3
votes
6
answers
675
views
6
answers
... If you're handy with Python, then [ETE Toolkit][1] will do this and more.
[1]: http://etetoolkit.org/ ...
written 10 months ago by
george.ry • 980
3
votes
1
answer
453
views
1
answers
Comment:
C: Multiple Sequence Alignment tools
... Unless I'm missing some complexity here, you don't need an MSA to achieve this. A local blast library will do this far more simply. ...
written 10 months ago by
george.ry • 980
1
vote
1
answer
365
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1
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... We need more information on what you're trying to do to answer this properly.
However, for 2), RepeatMasker significantly outperforms Censor. Unless you have a reason not to use it, RepeatMasker is basically the *de facto* standard. ...
written 11 months ago by
george.ry • 980
2
votes
2
answers
504
views
2
answers
... I actually end up doing this with some regularity, so here's a smooth all-in-one method:
samtools view -H yourfile.bam > header
then
samtools view yourfile.bam | split - yourprefix -l 8000000 --filter='cat header - > $FILE.sam'
or
samtools view yourfile.bam | split - yourp ...
written 12 months ago by
george.ry • 980
2
votes
8
answers
4.3k
views
8
answers
... A monumentally stupid day. Nothing else to say. ...
written 14 months ago by
george.ry • 980
0
votes
2
answers
1.4k
views
2
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... This should be an (the) answer, as it's really the only way to go about it!
If I had to re-format and re-write every file from which I extract random sequences, the storage array would have a fit! From a practical perspective, if you are actually storing data on a shared array with some kind of ba ...
written 14 months ago by
george.ry • 980
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For A: Script for extracting atomic position of nucleotide base
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