User: Rodrigo

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Rodrigo140
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Posts by Rodrigo

<prev • 13 results • page 1 of 2 • next >
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Comment: C: How to use biopython neighborsearch?
... I recommend you to try to learn python then at the same time you try to understand this code. I recommend you [this book][1]. Now, everything in the example prefixed by `Bio` is part of the `biopython` package. In the same manner, everything prefixed by `Bio.PDB` is part of the `PBB` module of `bio ...
written 12 weeks ago by Rodrigo140
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Answer: A: How to use biopython neighborsearch?
... Normally you should write down what have you tried so others understand the specifics of the problem. That being said, here is an concrete example for NeighborSearch. Suppose you have a PDB `1prot.pdb` in the current directory and want to find all residues at distance 5 angstroms from alpha carbon ...
written 12 weeks ago by Rodrigo140
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Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... The `-out` version is available for the version `2.1.10` so maybe is a matter of updating your FastTree version. Also the correct way would be to type in the command line `FastTree -nt -gtr -out test.out test.codon`. ...
written 12 weeks ago by Rodrigo140
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Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Ok I see thanks for the info. It actually has an option `-out`: > FastTree -out tree protein_alignment Where tree protein is your `.tree.` file and the protein_alignment your `.fasta` (in your case a `.codon` file). Have you tried running `FastTree -gtr -n -out 245_hypothetical_protein.codon 24 ...
written 12 weeks ago by Rodrigo140
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Comment: C: "out" parameter for _Fasttree module in Bio.Phylo.Applications from Biopython 1.
... Taken from FastTree docs: > By default FastTree expects protein alignments, use -nt for nucleotides and > -gtr -- generalized time-reversible model (nucleotide alignments only) It seems that both options `nt` and `gtr` are for nucleotide alignments and your file is a codon alignment. Tr ...
written 12 weeks ago by Rodrigo140
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Answer: A: Error ecountered while running conifer with demo data set
... I think is a bug with the source code of `conifer`. The error you get, Traceback (most recent call last): File "conifer_v0.2.2/conifer.py", line 682, in args.func(args) File "/conifer_v0.2.2/conifer.py", line 157, in CF_analyze probeIDs = np.array(map(operator.itemg ...
written 4 months ago by Rodrigo140
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Comment: C: why spectral clustering show a warning?
... How are you extracting the connected components from the matrix? are you then passing each of them as argument to the function? ...
written 4 months ago by Rodrigo140
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Comment: C: why spectral clustering show a warning?
... In graph theory, what you describe is called _complete graph_. I checked the [source code](http://pydoc.net/Python/scikit-learn/0.16.1/sklearn.manifold.spectral_embedding_/) (assuming you are using scikit-learn package, where we can find if not _graph_is_connected(adjacency): warnings.w ...
written 4 months ago by Rodrigo140
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Answer: A: How to extract polymorphic positions from several alignments?
... Supposing your sequences are the same length and have no empty spaces (no '--') as in your example, you can use the following (explained) script. # Start of script from collections import Counter from glob import glob import numpy as np from Bio import AlignIO Along with modul ...
written 4 months ago by Rodrigo140
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Comment: C: why spectral clustering show a warning?
... Well, depends on what format you're using for your graph (edgelist, csv, etc) but a couple of possibilities are, you can download `gephi` which is a software for displaying graphs in a beautiful way and you can also apply some cluster algorithms (spectral included) and see how the nodes mode while i ...
written 5 months ago by Rodrigo140

Latest awards to Rodrigo

Scholar 12 weeks ago, created an answer that has been accepted. For A: How to extract polymorphic positions from several alignments?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How to extract polymorphic positions from several alignments?
Scholar 4 months ago, created an answer that has been accepted. For A: How to extract polymorphic positions from several alignments?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to extract polymorphic positions from several alignments?

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