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Insert id from same block

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# 1  
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

# 2  
Old 05-17-2014
Is ID=value always the 1st element in the semicolon separated list in the last column on the lines that have gene or protein_coding_gene in the 3rd column, or can it appear later in the list or in an earlier column?
# 3  
Old 05-17-2014
I`m aware of this file type, it is also known as general feature format or gff .On behalf of OP i can say that
Code:
ID=value

is always the 1st element in the last semicolon separated string. For this particular file it will always be
Code:
ID=

as we can see. Sometimes it can also say
Code:
Name=

.. whatever it is, its consistent throughout the file.

Don, the short answer to your question is Yes.
# 4  
Old 05-18-2014
Hmmm, if the sample data is representative then it's not even necessary to take the "ID=" field from an earlier record. The value you want it already in the "ID=" field of the "exon" record. You just have to strip off the "_*" suffix.
# 5  
Old 05-18-2014
well, the id field in the exon rows may not always be of that form. It happens so in this case but they may be represented differently. the 'true gene id' is always in the gene row.
# 6  
Old 05-18-2014
Hello Don, the ID value is always the first part of the list separated by ;, it doesnt appear anywhere else
# 7  
Old 05-18-2014
The following seems to do what you want:
Code:
awk '
$3 == "gene" || $3 == "protein_coding_gene" {
	end = index($NF, ";")
	id = ";gene_id=" substr($NF, 4, end - 4)
}
$3 == "exon" {
	$0 = $0 id
}
1' file

If you want to run this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk, /usr/xpg6/bin/awk, or nawk.
This User Gave Thanks to Don Cragun For This Post:
gina.lizar
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