myvariant 1.0.0

简介

MyVariant.Info提供简单易用的REST web服务来查询/检索genetic 变量注释数据它的设计简单，注重性能。 myvariant是一个易于使用的python包装器，用于访问MyVariant.Info服务。

要求

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”)

可选依赖项

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

安装

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

版本历史记录

CHANGES.txt

教程

Access ClinVar Data from MyVariant.info Services (the raw ipynb file is here)

文件

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

用法

In[1]:importmyvariantIn[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]:_idcadd.phreddbsnp.rsidquerychr1:g.866422C>Tchr1:g.866422C>T14.310rs139210662chr1:g.876664G>Achr1:g.876664G>A9.971rs571654307chr1:g.69635G>Cchr1:g.69635G>C6.123rs541766448In[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]:_idvcf.altvcf.positionvcf.refqueryrs2500chr11:g.66397320A>GG66397320ARCV000083611chrX:g.38271176A>GG38271176ACOSM1392449chr19:g.30935013C>TT30935013CIn[15]:mv.querymany(['rs58991260','rs2500','NA_TEST'],scopes='dbsnp.rsid',fields='dbsnp')Finished.1inputquerytermsfoundnohit:['NA_TEST']Pass"returnall=True"toreturncompletelistsofduplicateormissingqueryterms.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}]

联系人

向我们提出任何问题或反馈：

• biothings@googlegroups.com（公开讨论）
• help@myvariant.info（私下联系开发人员）
• Github issues
• 在twitter上@myvariantinfo
• 用标记myvariant在BioStars.org上发布一个问题