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Tests now pass, 23andme exome vcf works. Adds logging for time out PLOS search.

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This commit is contained in:
Philipp Bayer
2014-09-15 19:01:57 +10:00
parent 0fdf8e142f
commit 463b3a6af3
4 changed files with 4 additions and 11 deletions
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3
app/workers/parsing.rb
View File

@@ -54,7 +54,6 @@ class Parsing
.reject { |line| line.start_with?('#') } # Skip comments
stats[:rows_without_comments] = rows.length
csv = send(:"parse_#{genotype.filetype.gsub('-', '_').downcase}", rows)
logger.info(csv)
known_chromosomes = ['MT', 'X', 'Y', (1..22).map(&:to_s)].flatten
csv.select! do |row|
# snp name
@@ -143,8 +142,8 @@ class Parsing
alleles = names.map{ |a| trans_dict[a]}.sort.join # becomes AC
[
fields[2],
fields[1],
fields[0],
fields[1],
alleles
]
end.compact # because the above next introduces nil.

1
app/workers/plos_search.rb
View File

@@ -40,6 +40,7 @@ class PlosSearch
result = client.search(snp.name, 0, 999)
end
rescue Timeout::Error
logger.error("API call timed out")
false
end
logger.info('Successfully called the API')

7
spec/integration/genotype_parsing_and_deleting_spec.rb
View File

@@ -36,17 +36,14 @@ describe 'genotype parsing', sidekiq: :inline do
['rs71252250', '15118', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
['rs75062661', '69511', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
['rs142727405', '663097', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
['rs144155419', '717587', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
['rs3131972', '752721', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
['rs61770172', '753269', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0],
['rs61770173', '753405', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0]
]
expect(snp_data).to match_array(expected)
user_snps = UserSnp.all
user_snp_genotypes = user_snps.map(&:local_genotype)
expected_genotypes = %w(AG AG AG GG CC AA AG GG AA)
expected_genotypes = %w(AG AG AG GG CC)
expect(user_snp_genotypes).to eq(expected_genotypes)
user_snps.each do |s|
expect(s.genotype_id).to eq(genotype.id)

4
test/data/23andmeexome_test.csv
View File

@@ -144,8 +144,4 @@
1 69270 . A G 74.12 MQFilter40;QDFilter2 AC=2;AF=1.00;AN=2;DP=250;DS;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.0;MQ=3.28;MQ0=241;QD=0.3;SNPEFF_AMINO_ACID_CHANGE=S108;SNPEFF_CODON_CHANGE=tcA/tcG;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_69037_69829;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=OR4F5;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000534990 GT:AD:DP:GQ:PL 1/1:207,35:250:11.99:107,12,0
1 69511 rs75062661 A G 1354.06 MQFilter40 AC=2;AF=1.00;AN=2;DB;DP=95;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.9665;MQ=25.29;MQ0=10;QD=14.25;SNPEFF_AMINO_ACID_CHANGE=T141A;SNPEFF_CODON_CHANGE=Aca/Gca;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_69091_70008;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=OR4F5;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000335137 GT:AD:DP:GQ:PL 1/1:1,93:95:99:1387,141,0
1 663097 rs142727405 G C 39.61 MQFilter40 AC=2;AF=1.00;AN=2;DB;DP=8;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.0;MQ=23.33;MQ0=2;QD=4.95;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_pseudogene;SNPEFF_GENE_NAME=CICP3;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000440782 GT:AD:DP:GQ:PL 1/1:3,5:8:6.02:71,6,0
1 717587 rs144155419 G A 79.91 PASS AB=0.714;AC=1;AF=0.50;AN=2;BaseQRankSum=-0.495;DB;DP=14;Dels=0.0;FS=2.963;HRun=2;HaplotypeScore=0.0;MQ=52.61;MQ0=0;MQRankSum=0.495;QD=5.71;ReadPosRankSum=0.354;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=AL669831.1;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000358533 GT:AD:DP:GQ:PL 0/1:10,4:14:99:110,0,345
1 752721 rs3131972 A G 58.29 MQFilter40 AB=0.25;AC=1;AF=0.50;AN=2;BaseQRankSum=-0.727;DB;DP=4;Dels=0.0;FS=0.0;HRun=3;HaplotypeScore=0.0;MQ=29.0;MQ0=0;MQRankSum=0.727;QD=14.57;ReadPosRankSum=0.727;SNPEFF_EFFECT=TRANSCRIPT;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=RP11-206L10.10;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000435300 GT:AD:DP:GQ:PL 0/1:1,3:4:21.40:88,0,21
1 753269 rs61770172 C G 704.16 MQFilter40 AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.0;MQ=19.61;MQ0=35;QD=10.83;SNPEFF_EFFECT=TRANSCRIPT;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=FAM87B;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000326734 GT:AD:DP:GQ:PL 1/1:0,65:65:66.16:737,66,0
1 753405 rs61770173 C A 54.43 MQFilter40;QDFilter2 AB=0.75;AC=1;AF=0.50;AN=2;BaseQRankSum=3.873;DB;DP=35;Dels=0.0;FS=0.0;HRun=0;HaplotypeScore=0.8667;MQ=37.88;MQ0=1;MQRankSum=-2.812;QD=1.56;ReadPosRankSum=-2.016;SNPEFF_EFFECT=TRANSCRIPT;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=FAM87B;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000326734 GT:AD:DP:GQ:PL 0/1:24,8:35:84.42:84,0,599
1 884091 rs142735174 C CACCCTGGTCCCCCTGGTCC 98.52 PASS AB=0.536;AC=1;AF=0.50;AN=2;BaseQRankSum=0.259;DB;DP=15;FS=0.0;HRun=0;HaplotypeScore=284.6099;IndelType=I;MQ=49.09;MQ0=0;MQRankSum=1.813;QD=6.57;ReadPosRankSum=2.205;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000342066 GT:AD:DP:GQ:PL 0/1:2,4:15:99:138,0,769
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