在熊貓數據框中讀取序列化的json

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我想從pandas數據框中的文件中讀取雙串行化的json對象。的json實施例是下面，在熊貓數據框中讀取序列化的json

{"input":"8\t140630920\t.\tC\tT\t840.948\t.","assembly_name":"GRCh37","end":140630920,"seq_region_name":"8","transcript_consequences":[{"source":"Ensembl","variant_allele":"T","cdna_end":770,"phenotypes":[{"source":"MIM_disease","end":140715299,"seq_region_name":"8","attrib_type":"Gene","external_id":612292,"strand":"-","phenotype":"BIRK-BAREL MENTAL RETARDATION DYSMORPHISM SYNDROME","type":"Gene","id":"ENSG00000169427","start":140613081},{"source":"OMIM","risk_allele":1,"end":140630920,"seq_region_name":"8","strand":"+","phenotype":"BIRK-BAREL SYNDROME","associated_gene":"KCNK9","variation_names":"rs121908332","type":"Variation","id":"rs121908332","start":140630920},{"source":"ClinVar","clinvar_clin_sig":"pathogenic","review_status":"no assertion criteria provided","risk_allele":"T","end":140630920,"seq_region_name":"8","external_id":"RCV000005007.1","associated_gene":"KCNK9","phenotype":"Birk Barel mental retardation dysmorphism syndrome","strand":"+","type":"Variation","id":"rs121908332","start":140630920}],"codons":"Ggg/Agg","protein_end":236,"strand":-1,"amino_acids":"G/R","cdna_start":770,"transcript_id":"ENST00000520439","cds_start":706,"gene_id":"ENSG00000169427","protein_start":236,"cds_end":706,"consequence_terms":["missense_variant"],"impact":"MODERATE"},{"source":"RefSeq","variant_allele":"T","cdna_end":770,"phenotypes":[{"source":"MIM_disease","end":140715299,"seq_region_name":"8","attrib_type":"Gene","external_id":612292,"strand":"-","phenotype":"BIRK-BAREL MENTAL RETARDATION DYSMORPHISM SYNDROME","type":"Gene","id":"ENSG00000169427","start":140613081},{"source":"OMIM","risk_allele":1,"end":140630920,"seq_region_name":"8","strand":"+","phenotype":"BIRK-BAREL SYNDROME","associated_gene":"KCNK9","variation_names":"rs121908332","type":"Variation","id":"rs121908332","start":140630920},{"source":"ClinVar","clinvar_clin_sig":"pathogenic","review_status":"no assertion criteria provided","risk_allele":"T","end":140630920,"seq_region_name":"8","external_id":"RCV000005007.1","associated_gene":"KCNK9","phenotype":"Birk Barel mental retardation dysmorphism syndrome","strand":"+","type":"Variation","id":"rs121908332","start":140630920}],"codons":"Ggg/Agg","protein_end":236,"strand":-1,"amino_acids":"G/R","cdna_start":770,"transcript_id":"NM_016601.2","cds_start":706,"gene_id":51305,"protein_start":236,"cds_end":706,"consequence_terms":["missense_variant"],"impact":"MODERATE"},{"source":"RefSeq","variant_allele":"T","cdna_end":764,"phenotypes":[{"source":"MIM_disease","end":140715299,"seq_region_name":"8","attrib_type":"Gene","external_id":612292,"strand":"-","phenotype":"BIRK-BAREL MENTAL RETARDATION DYSMORPHISM SYNDROME","type":"Gene","id":"ENSG00000169427","start":140613081},{"source":"OMIM","risk_allele":1,"end":140630920,"seq_region_name":"8","strand":"+","phenotype":"BIRK-BAREL SYNDROME","associated_gene":"KCNK9","variation_names":"rs121908332","type":"Variation","id":"rs121908332","start":140630920},{"source":"ClinVar","clinvar_clin_sig":"pathogenic","review_status":"no assertion criteria provided","risk_allele":"T","end":140630920,"seq_region_name":"8","external_id":"RCV000005007.1","associated_gene":"KCNK9","phenotype":"Birk Barel mental retardation dysmorphism syndrome","strand":"+","type":"Variation","id":"rs121908332","start":140630920}],"codons":"Ggg/Agg","protein_end":236,"strand":-1,"amino_acids":"G/R","cdna_start":764,"transcript_id":"XM_005250954.1","cds_start":706,"gene_id":51305,"protein_start":236,"cds_end":706,"consequence_terms":["missense_variant"],"impact":"MODERATE"},{"source":"Ensembl","variant_allele":"T","cdna_end":755,"phenotypes":[{"source":"MIM_disease","end":140715299,"seq_region_name":"8","attrib_type":"Gene","external_id":612292,"strand":"-","phenotype":"BIRK-BAREL MENTAL RETARDATION DYSMORPHISM SYNDROME","type":"Gene","id":"ENSG00000169427","start":140613081},{"source":"OMIM","risk_allele":1,"end":140630920,"seq_region_name":"8","strand":"+","phenotype":"BIRK-BAREL SYNDROME","associated_gene":"KCNK9","variation_names":"rs121908332","type":"Variation","id":"rs121908332","start":140630920},{"source":"ClinVar","clinvar_clin_sig":"pathogenic","review_status":"no assertion criteria provided","risk_allele":"T","end":140630920,"seq_region_name":"8","external_id":"RCV000005007.1","associated_gene":"KCNK9","phenotype":"Birk Barel mental retardation dysmorphism syndrome","strand":"+","type":"Variation","id":"rs121908332","start":140630920}],"codons":"Ggg/Agg","protein_end":236,"strand":-1,"amino_acids":"G/R","cdna_start":755,"transcript_id":"ENST00000522317","cds_start":706,"gene_id":"ENSG00000169427","protein_start":236,"cds_end":706,"consequence_terms":["missense_variant","NMD_transcript_variant"],"impact":"MODERATE"},{"source":"Ensembl","variant_allele":"T","cdna_end":770,"phenotypes":[{"source":"MIM_disease","end":140715299,"seq_region_name":"8","attrib_type":"Gene","external_id":612292,"strand":"-","phenotype":"BIRK-BAREL MENTAL RETARDATION DYSMORPHISM SYNDROME","type":"Gene","id":"ENSG00000169427","start":140613081},{"source":"OMIM","risk_allele":1,"end":140630920,"seq_region_name":"8","strand":"+","phenotype":"BIRK-BAREL SYNDROME","associated_gene":"KCNK9","variation_names":"rs121908332","type":"Variation","id":"rs121908332","start":140630920},{"source":"ClinVar","clinvar_clin_sig":"pathogenic","review_status":"no assertion criteria provided","risk_allele":"T","end":140630920,"seq_region_name":"8","external_id":"RCV000005007.1","associated_gene":"KCNK9","phenotype":"Birk Barel mental retardation dysmorphism syndrome","strand":"+","type":"Variation","id":"rs121908332","start":140630920}],"codons":"Ggg/Agg","protein_end":236,"strand":-1,"amino_acids":"G/R","cdna_start":770,"transcript_id":"ENST00000303015","cds_start":706,"gene_id":"ENSG00000169427","protein_start":236,"cds_end":706,"consequence_terms":["missense_variant"],"impact":"MODERATE"},{"gene_id":"ENSG00000169427","source":"Ensembl","distance":1672,"variant_allele":"T","phenotypes":[{"source":"MIM_disease","end":140715299,"seq_region_name":"8","attrib_type":"Gene","external_id":612292,"strand":"-","phenotype":"BIRK-BAREL MENTAL RETARDATION DYSMORPHISM SYNDROME","type":"Gene","id":"ENSG00000169427","start":140613081},{"source":"OMIM","risk_allele":1,"end":140630920,"seq_region_name":"8","strand":"+","phenotype":"BIRK-BAREL SYNDROME","associated_gene":"KCNK9","variation_names":"rs121908332","type":"Variation","id":"rs121908332","start":140630920},{"source":"ClinVar","clinvar_clin_sig":"pathogenic","review_status":"no assertion criteria provided","risk_allele":"T","end":140630920,"seq_region_name":"8","external_id":"RCV000005007.1","associated_gene":"KCNK9","phenotype":"Birk Barel mental retardation dysmorphism syndrome","strand":"+","type":"Variation","id":"rs121908332","start":140630920}],"consequence_terms":["upstream_gene_variant"],"strand":-1,"transcript_id":"ENST00000523477","impact":"MODIFIER"},{"gene_id":"ENSG00000169427","source":"Ensembl","distance":2630,"variant_allele":"T","phenotypes":[{"source":"MIM_disease","end":140715299,"seq_region_name":"8","attrib_type":"Gene","external_id":612292,"strand":"-","phenotype":"BIRK-BAREL MENTAL RETARDATION DYSMORPHISM SYNDROME","type":"Gene","id":"ENSG00000169427","start":140613081},{"source":"OMIM","risk_allele":1,"end":140630920,"seq_region_name":"8","strand":"+","phenotype":"BIRK-BAREL SYNDROME","associated_gene":"KCNK9","variation_names":"rs121908332","type":"Variation","id":"rs121908332","start":140630920},{"source":"ClinVar","clinvar_clin_sig":"pathogenic","review_status":"no assertion criteria provided","risk_allele":"T","end":140630920,"seq_region_name":"8","external_id":"RCV000005007.1","associated_gene":"KCNK9","phenotype":"Birk Barel mental retardation dysmorphism syndrome","strand":"+","type":"Variation","id":"rs121908332","start":140630920}],"consequence_terms":["upstream_gene_variant"],"strand":-1,"transcript_id":"ENST00000519923","impact":"MODIFIER"}],"strand":1,"id":"8_140630920_C/T","allele_string":"C/T","most_severe_consequence":"missense_variant","start":140630920}

使用大熊貓數據幀讀這篇文章，

dft = pd.read_json(filename, lines = True)

結果在表如下所示， Table generated by pandas read-json

然而，我想從提取信息['transcript_consequences']列，也可從['phenotypes']列出['transcript_consequences']列。

如何在熊貓數據框中實現這個功能？

來源

2016-12-23 nilesh

什麼是「雙連載」是什麼意思？ –

@John Zwinck我給出了一個我想處理json的例子..hope有幫助。謝謝 – nilesh

@nilesh做了我的建議工作？與您的實際數據有什麼特別的區別？ – erasmortg

一種選擇可能是以下幾點：

>>> import pandas as pd 
>>> jsona = pd.read_json('jsona.json') #here the file is named 'jsona.json' 
>>> transcript_consequences = jsona['transcript_consequences'].apply(pd.Series)

在這裏，我不知道這是否是有意還是無意，但似乎transcript_consequences[0]是相同的transcript_consequences[6]。

你可以做到以下幾點：

>>> phenotypes0 = pd.DataFrame(transcript_consequences.phenotypes[0]) #and so on 

>>> isinstance(phenotypes0,pd.DataFrame) 
True 
>>> isinstance(transcript_consequences,pd.DataFrame) 
True 
>>> isinstance(jsona,pd.DataFrame) 
True 

#in order to get one dataframe, concatenate and pass the dataframes in a list, like so: 
>>> pd.concat([transcript_consequences, phenotypes0], axis=1) #with more elements (more phenotypes) add them to the list

來源

2016-12-23 13:25:02 erasmortg

在熊貓數據框中讀取序列化的json

回答

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