Welcome to MyVariant.py’s documentation!

MyVariant.Info provides simple-to-use REST web services to query/retrieve 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 gene 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/biothings/myvariant.py

Version history

Tutorial

TODO

API

myvariant.alwayslist(value)[source]

If input value if not a list/tuple type, return it as a single value list.

Example:

>>> x = 'abc'
>>> for xx in alwayslist(x):
...     print xx
>>> x = ['abc', 'def']
>>> for xx in alwayslist(x):
...     print xx
myvariant.get_hgvs_from_vcf(input_vcf)[source]

From the input VCF file (filename or file handle), return a generator of genomic based HGVS ids.

Parameters:input_vcf – input VCF file, can be a filename or a file handle
Returns:a generator of genomic based HGVS ids. To get back a list instead, using list(get_hgvs_from_vcf(“your_vcf_file”))

Note

This is a lightweight VCF parser to return valid genomic-based HGVS ids from the input_vcf file. For more sophisticated VCF parser, consider using PyVCF module.

myvariant.format_hgvs(chrom, pos, ref, alt)[source]

get a valid hgvs name from VCF-style “chrom, pos, ref, alt” data.

Example:

>>> myvariant.format_hgvs("1", 35366, "C", "T")
>>> myvariant.format_hgvs("2", 17142, "G", "GA")
>>> myvariant.format_hgvs("MT", 8270, "CACCCCCTCT", "C")
>>> myvariant.format_hgvs("X", 107930849, "GGA", "C")
class myvariant.MyVariantInfo(url='http://myvariant.info/v1')[source]

This is the client for MyVariant.info web services. Example:

>>> mv = MyVariantInfo()
metadata(verbose=True, **kwargs)[source]

Return a dictionary of MyVariant.info metadata.

Example:

>>> metadata = mv.metadata()
set_caching(cache_db='myvariant_cache', verbose=True, **kwargs)[source]

Installs a local cache for all requests.

cache_db is the path to the local sqlite cache database.

stop_caching()[source]

Stop caching.

clear_cache()[source]

Clear the globally installed cache.

get_fields(search_term=None, verbose=True)[source]

Wrapper for http://myvariant.info/v1/metadata/fields

search_term is a case insensitive string to search for in available field names. If not provided, all available fields will be returned.

Example:

>>> mv.get_fields()
>>> mv.get_fields("rsid")
>>> mv.get_fields("sift")

Hint

This is useful to find out the field names you need to pass to fields parameter of other methods.

getvariant(vid, fields=None, **kwargs)[source]

Return the variant object for the give HGVS-based variant id. This is a wrapper for GET query of “/variant/<hgvsid>” service.

Parameters:
  • vid – an HGVS-based variant id. More about HGVS id.
  • fields – fields to return, a list or a comma-separated string. If not provided or fields=”all”, all available fields are returned. See here for all available fields.
Returns:

a variant object as a dictionary, or None if vid is not found.

Example:

>>> mv.getvariant('chr9:g.107620835G>A')
>>> mv.getvariant('chr9:g.107620835G>A', fields='dbnsfp.genename')
>>> mv.getvariant('chr9:g.107620835G>A', fields=['dbnsfp.genename', 'cadd.phred'])
>>> mv.getvariant('chr9:g.107620835G>A', fields='all')

Hint

The supported field names passed to fields parameter can be found from any full variant object (without fields, or fields=”all”). Note that field name supports dot notation for nested data structure as well, e.g. you can pass “dbnsfp.genename” or “cadd.phred”.

getvariants(vids, fields=None, **kwargs)[source]

Return the list of variant annotation objects for the given list of hgvs-base varaint ids. This is a wrapper for POST query of “/variant” service.

Parameters:
  • ids

    a list/tuple/iterable or a string of comma-separated HGVS ids. More about hgvs id.

  • fields

    fields to return, a list or a comma-separated string. If not provided or fields=”all”, all available fields are returned. See here for all available fields.

  • as_generator – if True, will yield the results in a generator.
  • as_dataframe – if True or 1 or 2, return object as DataFrame (requires Pandas). True or 1: using json_normalize 2 : using DataFrame.from_dict otherwise: return original json
  • df_index – if True (default), index returned DataFrame by ‘query’, otherwise, index by number. Only applicable if as_dataframe=True.
Returns:

a list of variant objects or a pandas DataFrame object (when as_dataframe is True)

Ref:

http://docs.myvariant.info/en/latest/doc/variant_annotation_service.html.

Example:

>>> vars = ['chr1:g.866422C>T',
...         'chr1:g.876664G>A',
...         'chr1:g.69635G>C',
...         'chr1:g.69869T>A',
...         'chr1:g.881918G>A',
...         'chr1:g.865625G>A',
...         'chr1:g.69892T>C',
...         'chr1:g.879381C>T',
...         'chr1:g.878330C>G']
>>> mv.getvariants(vars, fields="cadd.phred")
>>> mv.getvariants('chr1:g.876664G>A,chr1:g.881918G>A', fields="all")
>>> mv.getvariants(['chr1:g.876664G>A', 'chr1:g.881918G>A'], as_dataframe=True)

Hint

A large list of more than 1000 input ids will be sent to the backend web service in batches (1000 at a time), and then the results will be concatenated together. So, from the user-end, it’s exactly the same as passing a shorter list. You don’t need to worry about saturating our backend servers.

Hint

If you need to pass a very large list of input ids, you can pass a generator instead of a full list, which is more memory efficient.

query(q, **kwargs)[source]

Return the query result. This is a wrapper for GET query of “/query?q=<query>” service.

Parameters:
  • q

    a query string, detailed query syntax here.

  • fields

    fields to return, a list or a comma-separated string. If not provided or fields=”all”, all available fields are returned. See here for all available fields.

  • size – the maximum number of results to return (with a cap of 1000 at the moment). Default: 10.
  • skip – the number of results to skip. Default: 0.
  • sort – Prefix with “-” for descending order, otherwise in ascending order. Default: sort by matching scores in decending order.
  • as_dataframe – if True or 1 or 2, return object as DataFrame (requires Pandas). True or 1: using json_normalize 2 : using DataFrame.from_dict otherwise: return original json
  • fetch_all – if True, return a generator to all query results (unsorted). This can provide a very fast return of all hits from a large query. Server requests are done in blocks of 1000 and yielded individually. Each 1000 block of results must be yielded within 1 minute, otherwise the request will expire at server side.
Returns:

a dictionary with returned variant hits or a pandas DataFrame object (when as_dataframe is True) or a generator of all hits (when fetch_all is True)

Ref:

http://docs.myvariant.info/en/latest/doc/variant_query_service.html.

Example:

>>> mv.query('_exists_:dbsnp AND _exists_:cosmic')
>>> mv.query('dbnsfp.polyphen2.hdiv.score:>0.99 AND chrom:1')
>>> mv.query('cadd.phred:>50')
>>> mv.query('dbnsfp.genename:CDK2', size=5)
>>> mv.query('dbnsfp.genename:CDK2', fetch_all=True)
>>> mv.query('chrX:151073054-151383976')

Hint

By default, query method returns the first 10 hits if the matched hits are >10. If the total number of hits are less than 1000, you can increase the value for size parameter. For a query returns more than 1000 hits, you can pass “fetch_all=True” to return a generator of all matching hits (internally, those hits are requested from the server-side in blocks of 1000).

querymany(qterms, scopes=None, **kwargs)[source]

Return the batch query result. This is a wrapper for POST query of “/query” service.

Parameters:
  • qterms – a list/tuple/iterable of query terms, or a string of comma-separated query terms.
  • scopes

    specify the type (or types) of identifiers passed to qterms, either a list or a comma-separated fields to specify type of input qterms, e.g. “dbsnp.rsid”, “clinvar.rcv_accession”, [“dbsnp.rsid”, “cosmic.cosmic_id”]. See here for full list of supported fields.

  • fields

    fields to return, a list or a comma-separated string. If not provided or fields=”all”, all available fields are returned. See here for all available fields.

  • returnall – if True, return a dict of all related data, including dup. and missing qterms
  • verbose – if True (default), print out information about dup and missing qterms
  • as_dataframe – if True or 1 or 2, return object as DataFrame (requires Pandas). True or 1: using json_normalize 2 : using DataFrame.from_dict otherwise: return original json
  • df_index – if True (default), index returned DataFrame by ‘query’, otherwise, index by number. Only applicable if as_dataframe=True.
Returns:

a list of matching variant objects or a pandas DataFrame object.

Ref:

http://docs.myvariant.info/en/latest/doc/variant_query_service.html for available fields, extra kwargs and more.

Example:

>>> mv.querymany(['rs58991260', 'rs2500'], scopes='dbsnp.rsid')
>>> mv.querymany(['RCV000083620', 'RCV000083611', 'RCV000083584'], scopes='clinvar.rcv_accession')
>>> mv.querymany(['COSM1362966', 'COSM990046', 'COSM1392449'], scopes='cosmic.cosmic_id', fields='cosmic')
>>> mv.querymany(['COSM1362966', 'COSM990046', 'COSM1392449'], scopes='cosmic.cosmic_id',
...              fields='cosmic.tumor_site', as_dataframe=True)

Hint

querymany() is perfect for query variants based different ids, e.g. rsid, clinvar ids, etc.

Hint

Just like getvariants(), passing a large list of ids (>1000) to querymany() is perfectly fine.

Hint

If you need to pass a very large list of input qterms, you can pass a generator instead of a full list, which is more memory efficient.

Indices and tables