Hi,
I'm a beginner at Python and would really appreciate some help in how to
extract information from a vcf file.
The attached file consists of a lot of information on mutations, this one
though is just 2 rows and 10 columns (the real one has a lot more rows).
I want to extract the mRNA ID only if the mutation is missense. These two rows
(mutations) that I have attached happens to be missense but how do I say that
I'm not interested in the mutations that's not missense (they might be e.g.
synonymous). Also, how do I say that if a mutation starts with a # symbol I
don't want to include it (sometimes the chr starts with a hash).
vcf file: 2 rows, 10 columns.
col 0 col 1 col 2 col 3
col 4 col5 col6 col7
col8 col9
chromosome position . Reference ALT
position . some statistics and the ID:s not
important not important
The important column is 7 where the ID is, i.e.
refseq.functionalClass=missense. It's a missense mutation, so then I want to
extract refseq.name=NM_003137492, or I want to extract only the ID, which in
this case is NM_003137492.
Then I want to do exactly the same thing for all the other mutations, but only
for the missense mutations not the other ones. How do I accomplish that? Where
do I start?
Best,
Anna
4 69345 . C T 32 . 1kg.AD=0;1kg.AF=0.8865;1kg.AN=345;AC=1;AF=0.50;AN=2;BaseQRankSum=-6.432;DP=327;DS;Dels=0.00;FS=6.435;HRun=0;HaplotypeScore=5.0380;MQ=54.34;MQ0=13;MQRankSum=-5.3457;QD=2.65;ReadPosRankSum=-0.321;SB=-321.04;dbsnp.ID=rs43032118;dbsnp.dbSNPBuildID=112;hgid.AF=0.6754;refseq.changesAA=true;refseq.codingCoordStr=c.345C>T;refseq.codonCoord=234;refseq.functionalClass=missense;refseq.inCodingRegion=true;refseq.mrnaCoord=321;refseq.name=NM_003137492;refseq.name2=PQ3D2;refseq.positionType=CFD;refseq.proteinCoordStr=p.C132T;refseq.referenceAA=BRT;refseq.referenceCodon=DGF;refseq.spliceDist=321;refseq.transcriptStrand=+;refseq.variantAA=Ala;refseq.variantCodon=GCA GT:AD:DP:GQ:PL 1/1:134,32:765:99:56,1,4576
4 87342 . A G 57.7 . 1kg.AD=0;1kg.AF=1.0;1kg.AN=345;AC=2;AF=0.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=2;HaplotypeScore=0.0000;MQ=29.00;MQ0=0;QD=54.97;SB=-52.65;dbsnp.ID=rs6732096;dbsnp.dbSNPBuildID=136;hgid.AF=0.9567;refseq.changesAA=true;refseq.codingCoordStr=c.3207A>G;refseq.codonCoord=349;refseq.functionalClass=missense;refseq.inCodingRegion=true;refseq.mrnaCoord=4509;refseq.name=NM_132768;refseq.name2=PQR321;refseq.positionType=CDS;refseq.proteinCoordStr=p.O125R;refseq.referenceAA=Trp;refseq.referenceCodon=ATG;refseq.spliceDist=-45;refseq.transcriptStrand=+;refseq.variantAA=Arg;refseq.variantCodon=CTT GT:AD:DP:GQ:PL 0/1:0,5:5:2.02:67,9,1
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