User: Biojl
Biojl • 1.7k
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Posts by Biojl
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... I am able to generate the pyham_analysis object but one of the things I want to do is generate a TreeProfile for a specific HOG as explained here.
https://zoo.cs.ucl.ac.uk/tutorials/tutorial_pyHam_get_started.html#genomedef
It requires hog_of_interest = ham_analysis.get_hog_by_id(HOG_ID), there is ...
written 8 months ago by
Biojl • 1.7k
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... Hi, I am having trobules with the pyham library to access OMA database from python.
#Python3
from omadb import Client
c = Client()
prot_id = 'PADI1_HUMAN'
r = c.proteins[prot_id] # Can also be called as c.proteins.info(prot_id)
import pyham
# Initialise pyHam ...
written 8 months ago by
Biojl • 1.7k
• updated
8 months ago by
clement.train • 10
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Comment:
C: Download cdna sequences from OMA
... Thanks you very much! ...
written 15 months ago by
Biojl • 1.7k
0
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Comment:
C: Download cdna sequences from OMA
... There is not. I don't want to download a 2.4Gb compressed file and parse it every time I want the cDNA of a bunch of orthologs. There is an option to download all the ortholog protein sequences when you search a particular protein. I was looking for the same with cDNA. ...
written 15 months ago by
Biojl • 1.7k
0
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1
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391
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Comment:
C: Download cdna sequences from OMA
... Yes, this is what I did, but it would be nice to have a bulk download of cDNA for selected sequences, just as there is for proteins ...
written 15 months ago by
Biojl • 1.7k
3
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... Hi,
I am trying to obtain the cdna sequences for orthologs groups. There is a button for *Download: Fasta* but apparently it only works for the protein sequences. Does anybody know if there is a way to download them in bulk as opposed to download every single sequence individually?
...
written 15 months ago by
Biojl • 1.7k
• updated
15 months ago by
adrian.altenhoff • 630
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... Are your running codeml through biopython? Is relatively easy to parse the output: https://github.com/biopython/biopython/blob/master/Bio/Phylo/PAML/codeml.py
...
written 21 months ago by
Biojl • 1.7k
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... What about calculating a Log odds ratio (LOR) using a pre-defined area around your genes of interest. Count the number of TFBS in those regions and compare it against the whole genome and/or other genes not related to the modules you want to test, to correct for the effect of having genes around you ...
written 21 months ago by
Biojl • 1.7k
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... What did you do in the end? ...
written 21 months ago by
Biojl • 1.7k
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4
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998
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... You are working with MAC right? You have a weird file structure, it has \r (mac) and \n (unix). To fix them you have to remove the \r:
[jl@gaia drive-download-20180509T103851Z-001]$ tr -d '\r' < file1.txt > unixfile1.txt
[jl@gaia drive-download-20180509T103851Z-001]$ tr -d '\r' < ...
written 22 months ago by
Biojl • 1.7k
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