jeremymcrae / denovonear Goto Github PK

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.

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?