newgene

In [1]: import mygene
In [2]: mg = mygene.MyGeneInfo()

# by default, it uses http:
In [3]: mg.url
Out[3]: 'http://mygene.info/v3'

# switch to use https
In [4]: mg.url = 'https://mygene.info/v3'

newgene

# Just a short-hand to type less
alias f8='flake8'

# run "hgf" anywhere in a mercurial repo, it will check all changed *.py with flake8
alias hgf='tmp_cwd=`pwd` ; cd `hg root`; hgs -nmd |grep "\.py$" |xargs flake8; cd $tmp_cwd; unset tmp_cwd'

# run "gf" anywhere in a git repo, it will check all changed *.py with flake8
alias gf='tmp_cwd=`pwd` ; cd `git rev-parse --show-toplevel`; git diff --name-only |grep "\.py$" |xargs flake8; cd $tmp_cwd; unset tmp_cwd'

newgene

{
  "app_revision": "193:7417080ffb37",
  "available_fields": [
    "accession",
    "alias",
    "biocarta",
    "chr",
    "end",
    "ensemblgene",
    "ensemblprotein",

newgene

{
    "_id": "1017",
    "_timestamp": "2014-08-25T00:00:00",
    "accession": {
        "genomic": [
            "ABBA01008397",
            "AC025162",
            "AC034102",
            "AC_000144",
            "AF512553",

newgene

{
    "_id": "15:g.33905410A>G",
    "mutdb": {
        "chromEnd": 33905410,
        "dbsnp_id": "rs2229116",
        "allele2": "G",
        "uniprot_id": "VAR_011405",
        "allele1": "A",
        "mutpred_score": 0.384,
        "cosmic_id": null,

newgene

{
  "properties": {
    "AnimalQTLdb": {
      "type": "string",
      "index": "no",
      "include_in_all": false
    },
    "FLYBASE": {
      "type": "string",
      "index_name": "flybase",

newgene

Readme for this contest

General context of this contest

Human immune system produces a vast variety of antibodies in order to respond to the external stimuli. Next-generation sequencing technology allows researchers to obtain the sequences of all antibodies from a single person. Clustering these antibody sequences allows us to understand how an antibody is produced. However, the number of antibody sequences from a single sample can be up to 1 million scale. Clustering with such a big scale poses a big computation challenge.

Current algorithm

The current algorithm for clustering antibody sequences computes a pairwise distance matrix, and then perform a hierarchical clustering to group sequences into clusters. This algorithm is implemented in Python as provided clonify_contest.py script.

newgene