User: george.ry
george.ry • 1.0k
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Posts by george.ry
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... Get [datamash][1] ... it's invaluable!
`sort -k1,1 < inputfile | datamash -g1 collapse 2 > groups`
[1]: https://www.gnu.org/software/datamash/ ...
written 5 days ago by
george.ry • 1.0k
1
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211
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... For how many leaf nodes then, outside of this example dataset? ...
written 9 days ago by
george.ry • 1.0k
2
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3
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205
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3
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... You can also have a look at [UGENE][1] as an alternative to Geneious.
[1]: http://ugene.net/ ...
written 9 days ago by
george.ry • 1.0k
1
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0
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211
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... Before you get too involved you need to make sure what you're planning is practical, as you get a lot of bifurcating trees from surprisingly few leaf nodes (and if it's bifurcating + others then it's even worse). If your plan is to do some compute for goodness of fit etc on all of these, then you m ...
written 9 days ago by
george.ry • 1.0k
1
vote
1
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154
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1
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... from collections import defaultdict as dd
from Bio import SeqIO
import numpy as np
shuffles = dd(list)
for record in SeqIO.parse(open('firstperm.fasta'), 'fasta'):
id = record.id.split('_')[0]
shuffles[id].append(len(record))
for k, v in shuffles.items( ...
written 14 days ago by
george.ry • 1.0k
0
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2
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176
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2
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... This is technically an issue with a malformed GTF due to the GFF-->GTF conversion, rather than with the script per se - the GTF format is defined [here][1], and should always include `gene_id` and `transcript_id` (it should also end each line with a ';' character).
It'll be simplest to just repl ...
written 16 days ago by
george.ry • 1.0k
0
votes
2
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207
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2
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Comment:
C: Print line based on partial match
... It definitely will work, but you have to put `^` in front of the 5 letter sequences in `File1` ...
^ATGCC
^TTGCA
^GGAAC
If you don't want to use grep then any program that will separate based on user-defined barcodes - flexbar / etc - will do this for you. ...
written 6 weeks ago by
george.ry • 1.0k
0
votes
1
answer
169
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1
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... If you're not looking to call the variants as Medhat says, then [bam-readcount][1] will do this.
[1]: https://github.com/genome/bam-readcount ...
written 6 weeks ago by
george.ry • 1.0k
1
vote
4
answers
571
views
4
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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 9 months ago by
george.ry • 1.0k
3
votes
3
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1.5k
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3
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... 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 9 months ago by
george.ry • 1.0k
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