Package to examine de novo clustering
Project description
Denovonear
This code assesses whether de novo single-nucleotide variants are closer together within the coding sequence of a gene than expected by chance. We use local-sequence based mutation rates to account for differential mutability of regions. The default rates are per-trinucleotide based see Nature Genetics 46:944–950, but you can use your own rates, or even longer sequence contexts, such as 5-mers or 7-mers.
Install
pip install denovonear
Usage
Analyse de novo mutations with the CLI tool:
denovonear cluster \
--in data/example.grch38.dnms.txt \
--gencode data/example.grch38.gtf \
--fasta data/example.grch38.fa \
--out output.txt
explanation of options:
--in
: path to tab-separated table of de novo mutations. See example table below for columns, orexample.grch38.dnms.txt
in data folder.--gencode
: path to GENCODE annotations in GTF format for transcripts and exons e.g. example release. Can be gzipped, or uncompressed.--fasta
: path to genome fasta, matching genome build of gencode file
If the --gencode or --fasta options are skipped (e.g. denovonear cluster --in INFILE --out OUTFILE
), gene annotations will be retrieved via an ensembl web
service. For that, you might need to specify --genome-build grch38
to ensure
the gene coordinates match your de novo mutation coordinates.
--rates PATH_TO_RATES
--cache-folder PATH_TO_CACHE_DIR
--genome-build "grch37" or "grch38" (default=grch37)
The optional rates file is a table separated file with three columns: 'from', 'to', and 'mu_snp'. The 'from' column contains DNA sequence (where the length is an odd number) with the base to change at the central nucleotide. The 'to' column contains the sequence with the central base modified. The 'mu_snp' column contains the probability of the change (as per site per generation).
The cache folder defaults to making a folder named "cache" within the working directory. The genome build indicates which genome build the coordinates of the de novo variants are based on, and defaults to GRCh37.
Example de novo table
gene_name | chr | pos | consequence | snp_or_indel |
---|---|---|---|---|
OR4F5 | chr1 | 69500 | missense_variant | DENOVO-SNP |
OR4F5 | chr1 | 69450 | missense_variant | DENOVO-SNP |
Python usage
from denovonear.gencode import Gencode
from denovonear.cluster_test import cluster_de_novos
gencode = Gencode('./data/example.grch38.gtf', './data/example.grch38.fa')
symbol = 'OR4F5'
de_novos = {'missense': [69500, 69450, 69400], 'nonsense': []}
p_values = cluster_de_novos(symbol, de_novos, gencode[symbol], iterations=1000000)
Pull out site-specific rates by creating Transcript objects, then get the rates by consequence at each site
from denovonear.rate_limiter import RateLimiter
from denovonear.load_mutation_rates import load_mutation_rates
from denovonear.load_gene import construct_gene_object
from denovonear.site_specific_rates import SiteRates
# extract transcript coordinates and sequence from Ensembl
async with RateLimiter(per_second=15) as ensembl:
transcript = await construct_gene_object(ensembl, 'ENST00000346085')
mut_rates = load_mutation_rates()
rates = SiteRates(transcript, mut_rates)
# rates are stored by consequence, but you can iterate through to find all
# possible sites in and around the CDS:
for cq in ['missense', 'nonsense', 'splice_lof', 'synonymous']:
for site in rates[cq]:
site['pos'] = transcript.get_position_on_chrom(site['pos'], site['offset'])
# or if you just want the summed rate
rates['missense'].get_summed_rate()
Identify transcripts containing de novo events
You can identify transcripts containing de novos events with the
identify_transcripts.py
script. This either identifies all transcripts for a
gene with one or more de novo events, or identifies the minimal set of
transcripts to contain all de novos (where transcripts are prioritised on the
basis of number of de novo events, and length of coding sequence). Transcripts
can be identified with:
denovonear transcripts \
--de-novos data/example_de_novos.txt \
--out output.txt \
--all-transcripts
Other options are:
--minimise-transcripts
in place of--all-transcripts
, to find the minimal set of transcripts--genome-build "grch37" or "grch38" (default=grch37)
Gene or transcript based mutation rates
You can generate mutation rates for either the union of alternative transcripts
for a gene, or for a specific Ensembl transcript ID with the
construct_mutation_rates.py
script. Lof and missense mutation rates can be
generated with:
denovonear rates \
--genes data/example_gene_ids.txt \
--out output.txt
The tab-separated output file will contain one row per gene/transcript, with each line containing a transcript ID or gene symbol, a log10 transformed missense mutation rate, a log10 transformed nonsense mutation rate, and a log10 transformed synonymous mutation rate.
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