andrewyatz

Ensembl GraphQL

To find more information please see our docs or our public service schema explorer.

andrewyatz

#!/usr/bin/python3

import gzip
import sys

filename = sys.argv[1]
file = gzip.open(filename, "rt")

position = 0
contigous_n = 0

andrewyatz

Genome provider analysis

This is a selection of data and schema which can be used to investigate similarities/differences between the provided genomes files for GRCh38/hg38.

andrewyatz

andrewyatz

andrewyatz

openapi: 3.0.0
info:
  title: Species Search API
  description: An API for performing species searches to find species of question
  version: 1.0.0
tags:
  - name: search
    description: Search for genomes/species
paths:
  "/api/genome_search":

andrewyatz

{
  "$schema": "http://json-schema.org/draft-07/schema",
  "$id": "http://github.com/samtools/hts-specs/pub/refget-metadata.schema.1.0.0.json",
  "title": "Refget Metadata",
  "description": "Holds metadata pertaining to a record within the refget protocol",
  "type" : "object",
  "properties": {
    "id" : {
      "description": "The checksum identifier for a given record (the default)",
      "type" : "string"

andrewyatz

import xml.etree.cElementTree as ElementTree
import json, pytz, zipfile, unicodedata, re
from datetime import datetime
from os import listdir
from os.path import isfile, join
import glob

def slugify(value):
    """
    Normalizes string, converts to lowercase, removes non-alpha characters.

andrewyatz

Files

Files are downloaded from the MGnify resource and then processed using the calc.pl and checksum_checker.pl scripts. We also use the Unix commands awk and sort to format input into a santised format

Algorithm

• Process FASTA files
  • Read two lines at a time
  • Extract ID
  • Extract seq
• Calculate MD5 and TRUNC512

andrewyatz

#!/usr/bin/env perl
use strict;
use warnings;

use Bio::SeqIO;

my ($window_size, $fasta, $out) = @ARGV;

die "No window size given" if ! $window_size;
die "No fasta input" if ! $fasta;