Created
April 6, 2015 23:30
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arup duplicates
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| In [40]: from collections import defaultdict | |
| In [41]: data = defaultdict(list) | |
| In [42]: for row in json.load(open('arup.json')): | |
| data[getkey(row)].append(row) | |
| ....: | |
| In [43]: for vals in data.values(): | |
| if not all(v == vals[0] for v in vals): | |
| print json.dumps(vals, indent=2, sort_keys=True) | |
| print '\n-----------------------------\n\n' | |
| ....: | |
| [ | |
| { | |
| "alt": "A", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/20039896", | |
| "pmid": [ | |
| "20039896", | |
| "17344846" | |
| ], | |
| "protein_change": "p.V292M", | |
| "sequence_change": "c.874G>A" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43601830, | |
| "ref": "G" | |
| }, | |
| { | |
| "alt": "A", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/21655256", | |
| "pmid": [ | |
| "21655256" | |
| ], | |
| "protein_change": "p.V292M", | |
| "sequence_change": "c.874G>A" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43601830, | |
| "ref": "G" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "C", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15531714&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "16705552", | |
| "15531714" | |
| ], | |
| "protein_change": "p.M918T", | |
| "sequence_change": "c.2753T>C" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43617416, | |
| "ref": "T" | |
| }, | |
| { | |
| "alt": "C", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=7906866&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "19240193", | |
| "8880581", | |
| "10445857", | |
| "7906417", | |
| "7906866", | |
| "7824936", | |
| "15281979", | |
| "9242375", | |
| "10679286", | |
| "17848262", | |
| "22992277" | |
| ], | |
| "protein_change": "p.M918T", | |
| "sequence_change": "c.2753T>C" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43617416, | |
| "ref": "T" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11230481&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "11230481", | |
| "12016484", | |
| "12116277" | |
| ], | |
| "protein_change": "p.E768D", | |
| "sequence_change": "c.2304G>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43613840, | |
| "ref": "G" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.arup.utah.edu/dev/database/MEN2/unpublished.html", | |
| "pmid": null, | |
| "protein_change": "p.E768D", | |
| "sequence_change": "c.2304G>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43613840, | |
| "ref": "G" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "G", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12072055&dopt=AbstractPlus", | |
| "pmid": [ | |
| "12072055" | |
| ], | |
| "protein_change": "p.Q781R", | |
| "sequence_change": "c.2342A>G" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43613878, | |
| "ref": "A" | |
| }, | |
| { | |
| "alt": "G", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/23468374", | |
| "pmid": [ | |
| "23468374" | |
| ], | |
| "protein_change": "p.Q781R", | |
| "sequence_change": "c.2342A>G" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43613878, | |
| "ref": "A" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16705552&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "19826964", | |
| "16705552" | |
| ], | |
| "protein_change": "p.C620F", | |
| "sequence_change": "c.1859G>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609103, | |
| "ref": "G" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=7916559&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "8909322", | |
| "19443294", | |
| "20979234", | |
| "7916559", | |
| "18063059", | |
| "7874109", | |
| "18976013" | |
| ], | |
| "protein_change": "p.C620F", | |
| "sequence_change": "c.1859G>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609103, | |
| "ref": "G" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/18322301", | |
| "pmid": [ | |
| "18322301" | |
| ], | |
| "protein_change": "p.S649L", | |
| "sequence_change": "c.1946C>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609994, | |
| "ref": "C" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/18322301", | |
| "pmid": [ | |
| "18322301" | |
| ], | |
| "protein_change": "p.S649L", | |
| "sequence_change": "c.1946C>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609994, | |
| "ref": "C" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/19826964", | |
| "pmid": [ | |
| "19826964" | |
| ], | |
| "protein_change": "p.S649L", | |
| "sequence_change": "c.1946C>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609994, | |
| "ref": "C" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11230481&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "18322301", | |
| "19906784", | |
| "11230481", | |
| "15320968", | |
| "21551259" | |
| ], | |
| "protein_change": "p.S649L", | |
| "sequence_change": "c.1946C>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609994, | |
| "ref": "C" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=18058472&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "18058472" | |
| ], | |
| "protein_change": "p.S649L", | |
| "sequence_change": "c.1946C>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609994, | |
| "ref": "C" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=14718397&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "14718397" | |
| ], | |
| "protein_change": "p.D631D", | |
| "sequence_change": "c.1893C>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609941, | |
| "ref": "C" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/17344846", | |
| "pmid": [ | |
| "17344846" | |
| ], | |
| "protein_change": "p.D631D", | |
| "sequence_change": "c.1893C>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609941, | |
| "ref": "C" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "A", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/21810974", | |
| "pmid": [ | |
| "21810974" | |
| ], | |
| "protein_change": "p.V648I", | |
| "sequence_change": "c.1942G>A" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609990, | |
| "ref": "G" | |
| }, | |
| { | |
| "alt": "A", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Uncertain", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12466368&dopt=AbstractPlus", | |
| "pmid": [ | |
| "12466368", | |
| "18209889" | |
| ], | |
| "protein_change": "p.V648I", | |
| "sequence_change": "c.1942G>A" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609990, | |
| "ref": "G" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "A", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/21655256", | |
| "pmid": [ | |
| "21655256" | |
| ], | |
| "protein_change": "p.C634Y", | |
| "sequence_change": "c.1901G>A" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609949, | |
| "ref": "G" | |
| }, | |
| { | |
| "alt": "A", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/20080836", | |
| "pmid": [ | |
| "23330657", | |
| "20080836", | |
| "17610518" | |
| ], | |
| "protein_change": "p.C634Y", | |
| "sequence_change": "c.1901G>A" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609949, | |
| "ref": "G" | |
| }, | |
| { | |
| "alt": "A", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=8099202&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "12604374", | |
| "9230192", | |
| "19240193", | |
| "11524247", | |
| "8099202", | |
| "9820617", | |
| "7824936", | |
| "7491519", | |
| "12864791", | |
| "18063059", | |
| "7914213", | |
| "12711285" | |
| ], | |
| "protein_change": "p.C634Y", | |
| "sequence_change": "c.1901G>A" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609949, | |
| "ref": "G" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=7608256&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "14718397", | |
| "16839264", | |
| "18062802", | |
| "22274720", | |
| "10049754", | |
| "7608256", | |
| "24134185" | |
| ], | |
| "protein_change": "p.D631Y", | |
| "sequence_change": "c.1891G>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609939, | |
| "ref": "G" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11149622&ordinalpos=13&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum", | |
| "pmid": [ | |
| "11149622" | |
| ], | |
| "protein_change": "p.D631Y", | |
| "sequence_change": "c.1891G>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43609939, | |
| "ref": "G" | |
| } | |
| ] | |
| ----------------------------- | |
| [ | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=9506724&dopt=Abstract", | |
| "pmid": [ | |
| "18058472", | |
| "16388093", | |
| "17483988", | |
| "12566528", | |
| "17021738", | |
| "18062802", | |
| "9506724", | |
| "9090527", | |
| "12205548", | |
| "19826964", | |
| "19906784", | |
| "17102091", | |
| "15753368" | |
| ], | |
| "protein_change": "p.Y791F", | |
| "sequence_change": "c.2372A>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43613908, | |
| "ref": "A" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
| "external_links": "http://www.ncbi.nlm.nih.gov/pubmed/19826964", | |
| "pmid": [ | |
| "19826964" | |
| ], | |
| "protein_change": "p.Y791F", | |
| "sequence_change": "c.2372A>T" | |
| }, | |
| "transcript": "NM_020630.4" | |
| } | |
| ], | |
| "chrom": "chr10", | |
| "genome": "hg19", | |
| "offset": 43613908, | |
| "ref": "A" | |
| }, | |
| { | |
| "alt": "T", | |
| "annotations": [ | |
| { | |
| "annotator": "arup", | |
| "data": { | |
| "classification": "Pathogenic", | |
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| ----------------------------- |
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