[R] perl

[Sarah Goslee]

On Friday, November 28, 2014, Noha Osman <nmo_138 at usc.edu> wrote:

> Hi Folks
>
>
> Iam a new user in perl and I have two questions .Hopefully I get any help


Seems unlikely that  you'll get perl help on the R help list. Best try
again in a more appropriate forum.


>
>
> my data like that
>
>
> Chr1    TAIR10  chromosome      1       30427671        .       .       .
>      ID=Chr1;Name=Chr1
> Chr1    TAIR10  gene    3631    5899    .       +       .
>  ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
> Chr1    TAIR10  mRNA    3631    5899    .       +       .
>  ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
> Chr1    TAIR10  protein 3760    5630    .       +       .
>  ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
> Chr1    TAIR10  exon    3631    3913    .       +       .
>  Parent=AT1G01010.1
> Chr1    TAIR10  five_prime_UTR  3631    3759    .       +       .
>  Parent=AT1G01010.1
> Chr1    TAIR10  CDS     3760    3913    .       +       0
>  Parent=AT1G01010.1,AT1G01010.1-Protein;
> Chr1    TAIR10  exon    3996    4276    .       +       .
>  Parent=AT1G01010.1
> Chr1    TAIR10  CDS     3996    4276    .       +       2
>  Parent=AT1G01010.1,AT1G01010.1-Protein;
> Chr1    TAIR10  exon    4486    4605    .       +       .
>  Parent=AT1G01010.1
> Chr1    TAIR10  CDS     4486    4605    .       +       0
>  Parent=AT1G01010.1,AT1G01010.1-Protein;
> Chr1    TAIR10  exon    4706    5095    .       +       .
>  Parent=AT1G01010.1
> Chr1    TAIR10  CDS     4706    5095    .       +       0
>  Parent=AT1G01010.1,AT1G01010.1-Protein;
> Chr1    TAIR10  exon    5174    5326    .       +       .
>  Parent=AT1G01010.1
> Chr1    TAIR10  CDS     5174    5326    .       +       0
>  Parent=AT1G01010.1,AT1G01010.1-Protein;
>
> I need to use Hash  to answer these questions
>
> 1: output a file that has Gene name in column 1 and the number of exons it
> contains in column 2
>
> 2: output a file that list all the transcripts/mRNA in column 2 and the
> gene it is found in column 1
>
>
>
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>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

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