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Full Discussion: Insert id from same block
Top Forums Shell Programming and Scripting Insert id from same block Post 302902046 by gina.lizar on Saturday 17th of May 2014 07:01:17 PM
Old 05-17-2014
Insert id from same block
Hello all,

Please help modify my file. I want to pick up the ID value when the 3rd column is either gene or protein_coding_gene and place the ID in the gene_id attribute corresponding rows which has the the keyword exon in the third column.



Input file

Code:
10      ensembl gene    195359  195445  .       +       .       ID=GRMZM2G495457;biotype=transposable_element;logic_name=genebuilder
10 ensembl mRNA 195359 195445 . + . ID=GRMZM2G495457_T01;Parent=GRMZM2G495457;biotype=transposable_element;description=est;logic_name=genebuilder
10      .       exon    195359  195445  .       +       .       ID=GRMZM2G495457_E01;Parent=GRMZM2G495457_T01;constitutive=1;rank=1
10      ensembl protein_coding_gene    279670  280203  .       +       .       ID=GRMZM2G041102;biotype=transposable_element;logic_name=genebuilder
10 ensembl mRNA 279670 280203 . + . ID=GRMZM2G041102_T01;Parent=GRMZM2G041102;biotype=transposable_element;description=est;logic_name=genebuilder
10      .       exon    279670  280203  .       +       .       ID=GRMZM2G041102_E01;Parent=GRMZM2G041102_T01;constitutive=1;ensembl_end_phase=-1;rank=1
10      ensembl gene    270190  270594  .       -       .       ID=GRMZM2G310936;biotype=low_confidence;logic_name=genebuilder
10 ensembl mRNA 270190 270594 . - . ID=GRMZM2G310936_T01;Parent=GRMZM2G310936;biotype=low_confidence;description=abinitio;logic_name=genebuilder
10      .       CDS     270190  270339  .       -       0       ID=GRMZM2G310936_P01;Parent=GRMZM2G310936_T01;rank=3
10      .       exon    270190  270339  .       -       .       ID=GRMZM2G310936_E03;Parent=GRMZM2G310936_T01;constitutive=1;ensembl_end_phase=-1;rank=3
10      .       CDS     270383  270430  .       -       0       ID=GRMZM2G310936_P01;Parent=GRMZM2G310936_T01;rank=2
10      .       exon    270383  270430  .       -       .       ID=GRMZM2G310936_E02;Parent=GRMZM2G310936_T01;constitutive=1;rank=2
10      .       CDS     270502  270594  .       -       0       ID=GRMZM2G310936_P01;Parent=GRMZM2G310936_T01;rank=1
10      .       exon    270502  270594  .       -       .       ID=GRMZM2G310936_E01;Parent=GRMZM2G310936_T01;constitutive=1;rank=1

Desired output with picked up IDs in red, and inserted values in blue

Code:
10      ensembl gene    195359  195445  .       +       .        ID=GRMZM2G495457;biotype=transposable_element;logic_name=genebuilder
10 ensembl mRNA 195359 195445 . + .  ID=GRMZM2G495457_T01;Parent=GRMZM2G495457;biotype=transposable_element;description=est;logic_name=genebuilder
10      .       exon    195359  195445  .       +       .        ID=GRMZM2G495457_E01;Parent=GRMZM2G495457_T01;constitutive=1;rank=1;gene_id=GRMZM2G495457
10      ensembl protein_coding_gene    279670  280203  .       +       .        ID=GRMZM2G041102;biotype=transposable_element;logic_name=genebuilder
10 ensembl mRNA 279670 280203 . + .  ID=GRMZM2G041102_T01;Parent=GRMZM2G041102;biotype=transposable_element;description=est;logic_name=genebuilder
10      .       exon    279670  280203  .       +       .        ID=GRMZM2G041102_E01;Parent=GRMZM2G041102_T01;constitutive=1;ensembl_end_phase=-1;rank=1;gene_id=GRMZM2G041102
10      ensembl gene    270190  270594  .       -       .       ID=GRMZM2G310936;biotype=low_confidence;logic_name=genebuilder
10 ensembl mRNA 270190 270594 . - .  ID=GRMZM2G310936_T01;Parent=GRMZM2G310936;biotype=low_confidence;description=abinitio;logic_name=genebuilder
10      .       CDS     270190  270339  .       -       0       ID=GRMZM2G310936_P01;Parent=GRMZM2G310936_T01;rank=3
10      .       exon    270190  270339  .       -       .        ID=GRMZM2G310936_E03;Parent=GRMZM2G310936_T01;constitutive=1;ensembl_end_phase=-1;rank=3;gene_id=GRMZM2G310936
10      .       CDS     270383  270430  .       -       0       ID=GRMZM2G310936_P01;Parent=GRMZM2G310936_T01;rank=2
10      .       exon    270383  270430  .       -       .        ID=GRMZM2G310936_E02;Parent=GRMZM2G310936_T01;constitutive=1;rank=2;gene_id=GRMZM2G310936
10      .       CDS     270502  270594  .       -       0       ID=GRMZM2G310936_P01;Parent=GRMZM2G310936_T01;rank=1
10      .       exon    270502  270594  .       -       .        ID=GRMZM2G310936_E01;Parent=GRMZM2G310936_T01;constitutive=1;rank=1;gene_id=GRMZM2G310936

 

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