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Full Discussion: Getting non unique lines from concatenated files
Top Forums UNIX for Dummies Questions & Answers Getting non unique lines from concatenated files Post 302508416 by pawannoel on Monday 28th of March 2011 01:53:10 PM
Old 03-28-2011
@Bartus :
Yeah thats exactly why I was confused because I was thinking two different regex matches must be stored in different variables ... but seems like it can be done with just one too ...
Thanks for your comments .... Hva nice daySmilie

@pkabali :
I didnt recieve any questions from you so dont worry ... Good day!

---------- Post updated at 12:53 PM ---------- Previous update was at 04:09 AM ----------

@Bartus :
Hi Bartus, Hope all well ... I have another question .... Concerning slightly more detailed text manipulation but its time for me to learn ...
Sample file
Code:
levure5/levure5.raw.vcf:SK1.scplasm1    6153    .    T    C    222    .    DP=6039;AF1=1;CI95=1,1;DP4=2,2,1706,3565;MQ=33;FQ=-282;PV4=0.6,1,1,1    GT:PL:GQ    1/1:255,255,0:99
levure6/levure6.raw.vcf:SK1.scplasm1    6153    .    T    C    222    .    DP=4272;AF1=1;CI95=1,1;DP4=9,1,1250,2356;MQ=33;FQ=-282;PV4=0.00051,1,1,1    GT:PL:GQ    1/1:255,255,0:99
levure7/levure7.raw.vcf:SK1.scplasm1    6153    .    T    C    222    .    DP=2389;AF1=1;CI95=1,1;DP4=8,3,732,1343;MQ=33;FQ=-282;PV4=0.021,0.48,1,1    GT:PL:GQ    1/1:255,255,0:99
levure8/levure8.raw.vcf:SK1.scplasm1    6153    .    T    C    222    .    DP=2768;AF1=1;CI95=1,1;DP4=5,3,861,1559;MQ=33;FQ=-282;PV4=0.14,1,1,1    GT:PL:GQ    1/1:255,255,0:99
levure5/levure5.raw.vcf:SK1.chr08    558643    .    G    A    225    .    DP=449;AF1=0.5;CI95=0.5,0.5;DP4=122,120,93,58;MQ=44;FQ=225;PV4=0.037,1,1.8e-40,1    GT:PL:GQ    0/1:255,0,255:99
levure6/levure6.raw.vcf:SK1.chr08    558643    .    G    A    211    .    DP=371;AF1=0.5;CI95=0.5,0.5;DP4=115,96,64,47;MQ=44;FQ=214;PV4=0.64,1,9e-33,1    GT:PL:GQ    0/1:241,0,255:99
levure7/levure7.raw.vcf:SK1.chr08    558643    .    G    A    210    .    DP=152;AF1=0.5;CI95=0.5,0.5;DP4=44,47,32,15;MQ=45;FQ=213;PV4=0.031,1,7e-21,1    GT:PL:GQ    0/1:240,0,255:99
levure8/levure8.raw.vcf:SK1.chr08    558643    .    G    A    225    .    DP=208;AF1=0.5;CI95=0.5,0.5;DP4=49,69,29,46;MQ=45;FQ=225;PV4=0.76,1,1.1e-29,1    GT:PL:GQ    0/1:255,0,255:99
levure5/levure5.raw.vcf:SK1.chr08    558978    .    C    T    117    .    DP=436;AF1=0.5;CI95=0.5,0.5;DP4=157,45,87,55;MQ=44;FQ=120;PV4=0.0011,3.2e-71,1.8e-39,1    GT:PL:GQ    0/1:147,0,255:99
levure6/levure6.raw.vcf:SK1.chr08    558978    .    C    T    127    .    DP=352;AF1=0.5;CI95=0.5,0.5;DP4=121,45,71,44;MQ=42;FQ=130;PV4=0.052,4.2e-49,1.2e-23,1    GT:PL:GQ    0/1:157,0,255:99

So in the file in the $F[7] there is the DP4 subfeild, so that would be [3] subfeild inside $F[7]. Now if you look in the sample file what I cant understand is how do I split this particular subfield which has four values separated by commas into separate sub-subfeilds separated by tabs. So basically DP4 reports 4 values for the follwing 4 attributes.
Code:
DP4=fwd_ref_allele, rev_ref_allele, fwd_non_ref_allele, rev_non_ref_allele

I would basically want to report the comma separated values in each line of my file at DP4= as four separate tab delimited entries such as
Code:
fwd_ref_allele=value1[TAB]rev_ref_allele=value2[TAB]fwd_non_ref_allele=value3[TAB]rev_non_ref_allele=value4[TAB]

Once they apear as individual feilds, I can then it will be eaier for me to do calculations using your previous codes.

Thank you and let me know if you can provide some insight on such a problem of text manipulation in files.

Cheers ... Have a nice evening Smilie
 

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