Skip to main content

Python Client for MyVariant.Info services.

Project description

Intro

MyVariant.Info provides simple-to-use REST web services to query/retrieve genetic variant annotation data. It’s designed with simplicity and performance emphasized. myvariant, is an easy-to-use Python wrapper to access MyVariant.Info services.

Requirements

python >=2.6 (including python3)

requests (install using “pip install requests”)

Optional dependencies

pandas (install using “pip install pandas”) is required for returning a list of variant objects as DataFrame.

Installation

Option 1

pip install myvariant

Option 2

download/extract the source code and run:

python setup.py install
Option 3

install the latest code directly from the repository:

pip install -e git+https://github.com/Network-of-BioThings/myvariant.py

Version history

CHANGES.txt

Tutorial

TODO

Documentation

http://myvariant-py.readthedocs.org/

Usage

In [1]: import myvariant

In [2]: mv = myvariant.MyVariantInfo()

In [3]: mv.getvariant("chr7:g.140453134T>C")
Out[3]:  #output below is collapsed
{"_id": "chr7:g.140453134T>C",
 "_version": 1,
 "cadd": {...},
 "cosmic": {...},
 "dbnsfp": {...},
 "dbsnp": {...},
 "docm": {...},
 "mutdb": {...},
 "snpeff": {...},
 "vcf": {
    "alt": "C",
    "position": "140453134",
    "ref": "T"
 }}

In [4]: mv.getvariant("chr7:g.140453134T>C", fields='cosmic,snpeff')
Out[4]:
{'_id': 'chr7:g.140453134T>C',
 '_version': 1,
 'snpeff': {'ann': {'transcript_biotype': 'Coding',
   'gene_id': 'BRAF',
   'effect': 'missense_variant',
   'putative_impact': 'MODERATE',
   'cds': {'length': '2301', 'position': '1801'},
   'feature_type': 'transcript',
   'gene_name': 'BRAF',
   'feature_id': 'NM_004333.4',
   'hgvs_p': 'p.Lys601Glu',
   'hgvs_c': 'c.1801A>G',
   'rank': '15',
   'total': '18',
   'protein': {'length': '766', 'position': '601'},
   'cdna': {'length': '2946', 'position': '1862'}}},
 'cosmic': {'mut_freq': 0.07,
  'alt': 'G',
  'mut_nt': 'A>G',
  'tumor_site': 'upper_aerodigestive_tract',
  'ref': 'A',
  'chrom': '7',
  'hg19': {'start': 140453134, 'end': 140453134},
  'cosmic_id': 'COSM478'}
 }

In [5]: mv.getvariant("chr7:g.140453134T>C", fields=['cosmic.tumor_site', 'snpeff.ann.gene_name'])
Out[5]:
{'_id': 'chr7:g.140453134T>C',
 '_version': 1,
 'snpeff': {'ann': {'gene_name': 'BRAF'}},
 'cosmic': {'tumor_site': 'upper_aerodigestive_tract'}
}

In [6]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'])
Out[6]:
[{'_id': 'chr1:g.866422C>T',
   ...
 },
 {'_id': 'chr1:g.876664G>A',
  ...
 },
 {'_id': 'chr1:g.69635G>C',
  ...
 }]

In [7]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],
fields='cadd.phred,dbsnp.rsid')
Out[7]:
[{'query': 'chr1:g.866422C>T',
  '_id': 'chr1:g.866422C>T',
  'dbsnp': {'rsid': 'rs139210662'},
  'cadd': {'phred': 14.31}},
 {'query': 'chr1:g.876664G>A',
  '_id': 'chr1:g.876664G>A',
  'dbsnp': {'rsid': 'rs571654307'},
  'cadd': {'phred': 9.971}},
 {'query': 'chr1:g.69635G>C',
  '_id': 'chr1:g.69635G>C',
  'dbsnp': {'rsid': 'rs541766448'},
  'cadd': {'phred': 6.123}}]

In [8]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],
fields='cadd.phred,dbsnp.rsid', as_dataframe=True)
Out[8]:
                               _id  cadd.phred   dbsnp.rsid
query
chr1:g.866422C>T  chr1:g.866422C>T      14.310  rs139210662
chr1:g.876664G>A  chr1:g.876664G>A       9.971  rs571654307
chr1:g.69635G>C    chr1:g.69635G>C       6.123  rs541766448

In [9]: mv.query('dbsnp.rsid:rs58991260', fields='dbsnp')
Out[9]:
{'total': 1,
 'hits': [{'_score': 17.48471,
   '_id': 'chr1:g.218631822G>A',
   'dbsnp': {'class': 'SNV',
    'gmaf': 0.02157,
    'vartype': 'snp',
    'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
    'var_subtype': 'ts',
    'alleles': [{'freq': 0.9784, 'allele': 'G'},
     {'freq': 0.02157, 'allele': 'A'}],
    'allele_origin': 'unspecified',
    'chrom': '1',
    'hg19': {'start': 218631822, 'end': 218631823},
    'validated': True,
    'dbsnp_build': 129,
    'alt': 'A',
    'rsid': 'rs58991260',
    'ref': 'G'}}],
 'took': 24,
 'max_score': 17.48471}


In [10]: mv.query('snpeff.ann.gene_name:cdk2 AND dbnsfp.polyphen2.hdiv.pred:D',
fields='dbnsfp.polyphen2.hdiv')
Out[10]:
{'total': 1188,
 'hits': [{'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
      'pred': 'D',
      'score': 1.0}}},
   '_score': 8.343648,
   '_id': 'chr12:g.56359720C>T'},
  {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
      'pred': 'D',
      'score': [1.0, 0.957, 0.998]}}},
   '_score': 8.343648,
   '_id': 'chr12:g.56360819G>C'},

   ...

  {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
      'pred': 'D',
      'score': 1.0}}},
   '_score': 8.343648,
   '_id': 'chr12:g.56360853G>A'}],
   'took': 3521,
   'max_score': 8.343648}


In [11]: mv.query('chr1:69000-70000', fields='cadd.phred')
Out[11]:
{'total': 3,
 'hits': [
  {'_score': 14.155852, '_id': 'chr1:g.69428T>G', 'cadd': {'phred': 12.14}},
  {'_score': 14.148425, '_id': 'chr1:g.69511A>G', 'cadd': {'phred': 8.98}},
  {'_score': 3.5420983, '_id': 'chr1:g.69538G>A', 'cadd': {'phred': 7.339}}],
 'took': 725,
 'max_score': 14.155852}

In [12]: mv.querymany(['rs58991260', 'rs2500'], scopes='dbsnp.rsid', fields='dbsnp')
Finished.
Out[12]:
[{'query': 'rs58991260',
  '_id': 'chr1:g.218631822G>A',
  'dbsnp': {'class': 'SNV',
   'gmaf': 0.02157,
   'vartype': 'snp',
   'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
   'var_subtype': 'ts',
   'alleles': [{'freq': 0.9784, 'allele': 'G'},
    {'freq': 0.02157, 'allele': 'A'}],
   'allele_origin': 'unspecified',
   'chrom': '1',
   'hg19': {'start': 218631822, 'end': 218631823},
   'validated': True,
   'dbsnp_build': 129,
   'alt': 'A',
   'rsid': 'rs58991260',
   'ref': 'G'}},
 {'query': 'rs2500',
  '_id': 'chr11:g.66397320A>G',
  'dbsnp': {'class': 'SNV',
   'vartype': 'snp',
   'flags': ['ASP', 'INT', 'RV', 'U3'],
   'var_subtype': 'ts',
   'alleles': [{'allele': 'A'}, {'allele': 'G'}],
   'allele_origin': 'unspecified',
   'chrom': '11',
   'hg19': {'start': 66397320, 'end': 66397321},
   'dbsnp_build': 36,
   'alt': 'G',
   'ref': 'A',
   'rsid': 'rs2500',
   'validated': False}}]

In [13]: mv.querymany(['RCV000083620', 'RCV000083584'],
scopes='clinvar.rcv_accession', fields='clinvar')
Finished.
Out[13]:
[{'query': 'RCV000083620',
  'clinvar': {'type': 'single nucleotide variant',
   'gene': {'id': 5009, 'symbol': 'OTC'},
   'origin': 'unknown',
   'last_evaluated': 'None',
   'other_ids': 'dbSNP:72558473;',
   'clinvar_id': 97371,
   'hgvs': {'genomic': ['NG_008471.1:g.64470C>T',
     'NC_000023.11:g.38411952C>T',
     'NC_000023.10:g.38271205C>T'],
    'coding': 'NM_000531.5:c.958C>T'},
   'chrom': 'X',
   'cytogenic': 'Xp11.4',
   'name': 'NM_000531.5(OTC):c.958C>T (p.Arg320Ter)',
   'number_submitters': 1,
   'alt': 'T',
   'hg19': {'start': 38271205, 'end': 38271205},
   'allele_id': 103263,
   'rcv_accession': 'RCV000083620',
   'review_status': 'classified by single submitter',
   'clinical_significance': 'Pathogenic',
   'rsid': 'rs72558473',
   'ref': 'C'},
  '_id': 'chrX:g.38271205C>T'},
 {'query': 'RCV000083584',
  'clinvar': {'type': 'Deletion',
   'gene': {'id': 5009, 'symbol': 'OTC'},
   'origin': 'unknown',
   'last_evaluated': 'None',
   'other_ids': 'dbSNP:72558452;',
   'clinvar_id': 97337,
   'hgvs': {'genomic': ['NG_008471.1:g.61493_61495delGAG',
     'NC_000023.11:g.38408975_38408977delGAG',
     'NC_000023.10:g.38268228_38268230delGAG'],
    'coding': 'NM_000531.5:c.817_819delGAG'},
   'chrom': 'X',
   'cytogenic': 'Xp11.4',
   'name': 'NM_000531.5(OTC):c.817_819delGAG (p.Glu273del)',
   'number_submitters': 1,
   'alt': '-',
   'hg19': {'start': 38268228, 'end': 38268230},
   'allele_id': 103229,
   'rcv_accession': 'RCV000083584',
   'review_status': 'classified by single submitter',
   'clinical_significance': 'Pathogenic',
   'rsid': 'rs72558452',
   'ref': 'GAG'},
  '_id': 'chrX:g.38268228_38268230del'}]

In [14]: mv.querymany(['rs2500', 'RCV000083611', 'COSM1392449'],
scopes='clinvar.rcv_accession,dbsnp.rsid,cosmic.cosmic_id', fields='vcf', as_dataframe=1)
Finished.
Out[14]:
                              _id vcf.alt vcf.position vcf.ref
query
rs2500        chr11:g.66397320A>G       G     66397320       A
RCV000083611   chrX:g.38271176A>G       G     38271176       A
COSM1392449   chr19:g.30935013C>T       T     30935013       C


In [15]: mv.querymany(['rs58991260', 'rs2500', 'NA_TEST'], scopes='dbsnp.rsid', fields='dbsnp')
Finished.
1 input query terms found no hit:
        ['NA_TEST']
Pass "returnall=True" to return complete lists of duplicate or missing query terms.
Out[15]:
[{'query': 'rs58991260',
  '_id': 'chr1:g.218631822G>A',
  'dbsnp': {'class': 'SNV',
   'gmaf': 0.02157,
   'vartype': 'snp',
   'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
   'var_subtype': 'ts',
   'alleles': [{'freq': 0.9784, 'allele': 'G'},
    {'freq': 0.02157, 'allele': 'A'}],
   'allele_origin': 'unspecified',
   'chrom': '1',
   'hg19': {'start': 218631822, 'end': 218631823},
   'validated': True,
   'dbsnp_build': 129,
   'alt': 'A',
   'rsid': 'rs58991260',
   'ref': 'G'}},
 {'query': 'rs2500',
  '_id': 'chr11:g.66397320A>G',
  'dbsnp': {'class': 'SNV',
   'vartype': 'snp',
   'flags': ['ASP', 'INT', 'RV', 'U3'],
   'var_subtype': 'ts',
   'alleles': [{'allele': 'A'}, {'allele': 'G'}],
   'allele_origin': 'unspecified',
   'chrom': '11',
   'hg19': {'start': 66397320, 'end': 66397321},
   'dbsnp_build': 36,
   'alt': 'G',
   'ref': 'A',
   'rsid': 'rs2500',
   'validated': False}},
 {'query': 'NA_TEST', 'notfound': True}]

Contact

Drop us any feedback at: help@myvariant.info or on twitter @myvariantinfo.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

myvariant-0.1.1.tar.gz (10.5 kB view hashes)

Uploaded source

Built Distribution

myvariant-0.1.1-py2.py3-none-any.whl (13.8 kB view hashes)

Uploaded 2 7

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page