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License: MIT License
analysing proximity clustering of de novo variants in genes
License: MIT License
Occasionally, we can get an error when combining transcripts
import tempfile
from denovonear.load_gene import construct_gene_object
from denovonear.ensembl_requester import EnsemblRequest
cache = tempfile.TemporaryDirectory()
ensembl = EnsemblRequest(cache.name, 'grch37')
tx1 = construct_gene_object(ensembl, 'ENST00000432832')
tx2 = construct_gene_object(ensembl, 'ENST00000344777')
tx3 = construct_gene_object(ensembl, 'ENST00000553600')
combined = tx1 + tx2
# this gives an error! Only occurs after tx1 and tx2 have been combined
combined = tx3 + combined
# but this does not, even though they should be identical
combined = combined + tx3
The error given is
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
File "denovonear/transcript.pyx", line 221, in denovonear.transcript.Transcript.__add__
File "denovonear/transcript.pyx", line 326, in denovonear.transcript.Transcript.add_genomic_sequence
IndexError: basic_string::substr
Hi,
i installed both denovonear and fitDNM, and it looks like "EnsemblRequest" is not getting imported (called by mutation_rates.py). I checked "from denovonear.ensembl_requester import EnsemblRequest", and ensembl_requester does not seem to include EnsemblRequest. Can you point to me where EnsemblRequest is defined?
Hi Jeremy,
I got the mutation rate table link from the paper: De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies (http://science.sciencemag.org/content/350/6265/1262.full)
I just found that the link to download the mutation rate table has removed to a new directory.
The previous link is : https://github.com/jeremymcrae/denovonear/blob/master/data/forSanger_1KG_mutation_rate_table.txt
which is no more available.
Now the new link is https://github.com/jeremymcrae/denovonear/tree/master/denovonear/data/rates.txt
I'm wondering if the rate table version stays the same? Can I have the reason why the link changed please? We use that tab in our work and what to cite it in our paper.
In advance, thanks for your reply.
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