Question: how to write for getting set of gene in one line having each sample name
0
gravatar for raya.girish
22 months ago by
raya.girish20
raya.girish20 wrote:

Dear All It may be useless question I have data sheet having CNV information

File    CN State    Genes       Microarray Nomenclature

s1             1,33                a,b,c                Xq28(154,337,224-154,929,412)x1-2

s1             1.33                a,f,h                 Xp22.33(177,941-2,699,968)x2

s2             3.0                  r,h,s                 12p12.3p12.1(19,251,491-23,210,281)x2-3

s3             2.1                 a,t,c,a,r            12p11.22p11.21(28,433,320-32,514,115)x2-3

I am looking for code

Which will give me excel sheet contain

File    CN State    Genes       Microarray Nomenclature

s1             1.33                a                  Xq28(154,337,224-154,929,412)x1-2

s1             1.33                b                    Xq28(154,337,224-154,929,412)x1-2

s1             1.33                c                    Xq28(154,337,224-154,929,412)x1-2

Similar for other samples . This means that the set of gene will be split in new line but sample name , cnv status and nomenclature should also repeat once the gene set is split in new line

cnv R • 612 views
ADD COMMENTlink modified 22 months ago by Pierre Lindenbaum120k • written 22 months ago by raya.girish20

I see you tagged R, so you prefer to use R? Any experience with it?

ADD REPLYlink written 22 months ago by WouterDeCoster39k

nothing like that I am ostly working on R so

ADD REPLYlink written 22 months ago by raya.girish20
2
gravatar for Pierre Lindenbaum
22 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:
 awk '{n=split($3,a,/,/);for(i=1;i<=n;++i) {printf("%s\t%s\t%s\t%s\n",$1,$2,a[i],$4);}}' input.txt

File    CN State    Genes       Microarray Nomenclature
s1  1,33    a   Xq28(154,337,224-154,929,412)x1-2
s1  1,33    b   Xq28(154,337,224-154,929,412)x1-2
s1  1,33    c   Xq28(154,337,224-154,929,412)x1-2
s1  1.33    a   Xp22.33(177,941-2,699,968)x2
s1  1.33    f   Xp22.33(177,941-2,699,968)x2
s1  1.33    h   Xp22.33(177,941-2,699,968)x2
s2  3.0 r   12p12.3p12.1(19,251,491-23,210,281)x2-3
s2  3.0 h   12p12.3p12.1(19,251,491-23,210,281)x2-3
s2  3.0 s   12p12.3p12.1(19,251,491-23,210,281)x2-3
s3  2.1 a   12p11.22p11.21(28,433,320-32,514,115)x2-3
s3  2.1 t   12p11.22p11.21(28,433,320-32,514,115)x2-3
s3  2.1 c   12p11.22p11.21(28,433,320-32,514,115)x2-3
s3  2.1 a   12p11.22p11.21(28,433,320-32,514,115)x2-3
s3  2.1 r   12p11.22p11.21(28,433,320-32,514,115)x2-3
ADD COMMENTlink modified 22 months ago • written 22 months ago by Pierre Lindenbaum120k

hi pierre This code is not giving me gene at one line only one gene is getting printed

ADD REPLYlink written 22 months ago by raya.girish20

I have gene number in more than 20 gene seperated by ,

ADD REPLYlink written 22 months ago by raya.girish20
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