User: george.ry

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george.ry1.0k
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Posts by george.ry

<prev • 95 results • page 1 of 10 • next >
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Answer: A: problem in fetching data using excel
... 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.ry1.0k
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Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... For how many leaf nodes then, outside of this example dataset? ...
written 9 days ago by george.ry1.0k
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Answer: A: Any alternative (free, open source tool) for Geneious software for phylogenetic
... You can also have a look at [UGENE][1] as an alternative to Geneious. [1]: http://ugene.net/ ...
written 9 days ago by george.ry1.0k
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Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... 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.ry1.0k
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Answer: A: Computing chunk of fasta file before moving to next chunks using python
... 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.ry1.0k
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Comment: C: How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... 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.ry1.0k
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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.ry1.0k
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Answer: A: frequency of each nucleotide at each position in sequence
... 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.ry1.0k
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Answer: A: Run a Python program in Ubuntu
... 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.ry1.0k
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Answer: A: Error while downloading data using SRA toolkit
... 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.ry1.0k

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Guru 9 days ago, received more than 100 upvotes.
Scholar 9 days ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 13 days ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 9 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 10 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Scholar 19 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Pundit 23 months ago, created a comment with more than 10 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Appreciated 23 months ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
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Appreciated 23 months ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Teacher 23 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 2.4 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 2.6 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Affymetrix Cel File - Probe Intensity Values To Rgb
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Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: How To Identify Quantile Normalized Expression Data

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