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Return to: nCoV - discussion |
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#Post#: 282-------------------------------------------------- |
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covidcg.org's big file encoding Gisaid but hiding the names and |
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not showing the NNNNN |
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By: babar Date: January 17, 2021, 1:23 am |
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Download and unzip |
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https://storage.googleapis.com/ve-public/v1.4/data_package.json.gz |
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Then with node.js (on my laptop the file is too big for |
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chrome) |
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[code] |
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var t = require('./data_package.json'); |
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var fr_loc = {}; |
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var c =t["geo_select_tree"].children[2].children[15].children; |
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// list of French locations |
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for (var i=0;i<c.length;i++) { |
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if (c[i]) { |
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fr_loc[c[i].location_id]=c[i].label; |
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for (var j=0;j<c[i].children.length;j++) { |
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if (c[i].children[j]) |
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fr_loc[c[i].children[j].location_id]=c[i].label; |
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} |
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} |
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} |
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var fr_sequences=[]; |
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for (var i = 0;i < t.case_data.length; i++) { |
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if (fr_loc[t.case_data[i].location_id]) |
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fr_sequences.push(t.case_data[i]); |
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} |
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var lab_count = {}; |
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for (var i =0;i < fr_sequences.length; i++) { |
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var l = |
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t.metadata_map.submitting_lab[fr_sequences[i].submitting_lab]; |
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if (!lab_count[l]) lab_count[l]=0; |
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lab_count[l]++; |
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} |
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lab_count; |
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var SNP= {}; |
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for (var n in t.metadata_map.dna_snp) { |
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if (t.metadata_map.dna_snp.hasOwnProperty(n)) { |
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SNP[t.metadata_map.dna_snp[n]]=n; |
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} |
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} |
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for (var i =0;i < fr_sequences.length; i++) { |
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var mut = []; |
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for (var j =0; j<fr_sequences[i].dna_snp_str.length;j++) { |
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mut.push(SNP[fr_sequences[i].dna_snp_str[j]]); |
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} |
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fr_sequences[i].mut = mut; |
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fr_sequences[i].loc = fr_loc[fr_sequences[i].location_id]; |
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} |
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[/code] |
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output : a table of 2753 sequences, the first one is |
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[code] |
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> fr_sequences[0] |
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{ 'Accession ID': '2d58d2cd', |
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collection_date: '2020-02-26', |
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submission_date: '2020-03-14', |
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gender: 0, |
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age_start: 36, |
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age_end: 37, |
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patient_status: 0, |
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passage: 0, |
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specimen: 5, |
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lineage: 'A.2', |
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clade: 'S', |
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sequencing_tech: 7, |
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assembly_method: 23, |
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comment_type: -1, |
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authors: 39, |
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originating_lab: 51, |
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submitting_lab: 30, |
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dna_snp_str: [ 28245, 28855, 4217, 14839, 15498, 18708, 19358, |
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19677 ], |
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gene_aa_snp_str: [ 14838, 4890, 18663, 18297, 19910, 605 ], |
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protein_aa_snp_str: [ 11687, 13956, 13590, 15422, 605, 15820 |
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], |
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location_id: 1315, |
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mut: |
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[ '8782|C|T', |
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'9477|T|A', |
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'14805|C|T', |
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'25553|C|T', |
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'25979|G|T', |
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'28144|T|C', |
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'28657|C|T', |
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'28863|C|T' ] |
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loc:'Grand-Est'} |
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[/code] |
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#Post#: 283-------------------------------------------------- |
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Re: covidcg.org's big file encoding Gisaid but hiding the names |
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and not showing the NNNNN |
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By: gsgs Date: January 17, 2021, 4:49 am |
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hi babar. |
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Thanks ! |
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I could download and unzip that file. |
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https://storage.googleapis.com/ve-public/v1.5/data_package.json.gz |
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231MB , 341354 lines , |
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https://storage.googleapis.com/ve-public/v1.6/data_package.json.gz |
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https://storage.googleapis.com/ve-public/v1.7/data_package.json.gz |
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. |
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396 with B.1.351 |
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shall we use (part of) this forum to exchange sequencing info ? |
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or make another forum ? |
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shall I make you admin for re-organisation ? |
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shall we invite others ? |
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