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myvariant
Artifacts are distributable versions of a package. It typically includes the source code and metadata
Advanced tools
- Version
- 1.0.0
- Maintainers
- 2
.. image:: https://badge.fury.io/py/myvariant.svg :target: https://pypi.org/project/myvariant/
.. image:: https://img.shields.io/pypi/pyversions/myvariant.svg :target: https://pypi.org/project/myvariant/
.. image:: https://img.shields.io/pypi/format/myvariant.svg :target: https://pypi.org/project/myvariant/
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.
.. _MyVariant.Info: http://myvariant.info .. _biothings_client: https://pypi.org/project/biothings-client/ .. _myvariant: https://pypi.org/project/myvariant/
.. Note::
As of v1.0.0, myvariant_ Python package is now a thin wrapper of underlying biothings_client_ package,
a universal Python client for all BioThings APIs <http://biothings.io>, including MyVariant.info.
The installation of myvariant_ will install biothings_client_ automatically. The following code snippets
are essentially equivalent:
* Continue using myvariant_ package
.. code-block:: python
In [1]: import myvariant
In [2]: mv = myvariant.MyVariantInfo()
* Use biothings_client_ package directly
.. code-block:: python
In [1]: from biothings_client import get_client
In [2]: mv = get_client('variant')
After that, the use of ``mv`` instance is exactly the same, e.g. the usage examples below.
Requirements
python >=2.7 (including python3)
(Python 2.6 might still work, not it's not supported any more since v4.0.0.)
biothings_client_ (>=0.2.0, install using "pip install biothings_client")
Optional dependencies
`pandas <http://pandas.pydata.org>`_ (install using "pip install pandas") is required
for returning a list of variant objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#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/biothings/myvariant.py#egg=myvariant
Version history
`CHANGES.txt <https://raw.githubusercontent.com/biothings/myvariant.py/master/CHANGES.txt>`_
Tutorial
`Access ClinVar Data from MyVariant.info Services <https://cdn.rawgit.com/biothings/myvariant.info/master/docs/ipynb/myvariant_clinvar_demo.html>`_ (the raw ipynb file is `here <https://raw.githubusercontent.com/biothings/myvariant.info/master/docs/ipynb/myvariant_clinvar_demo.ipynb>`_)
Documentation
http://myvariant-py.readthedocs.org/
Usage
.. code-block:: python
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 question or feedback:
* biothings@googlegroups.com (public discussion)
* help@myvariant.info (reach devs privately)
* Github issues <https://github.com/biothings/myvariant.info/issues>_
* on twitter @myvariantinfo <https://twitter.com/myvariantinfo>_
* Post a question on BioStars.org <https://www.biostars.org/p/new/post/?tag_val=myvariant>_ with tag #myvariant.
FAQs
Python Client for MyVariant.Info services.
We found that myvariant demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
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