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Full Discussion: Grep and print only certain columns from a row
Top Forums Shell Programming and Scripting Grep and print only certain columns from a row Post 302845799 by jacobs.smith on Thursday 22nd of August 2013 10:06:37 AM
Old 08-22-2013
Quote:
Originally Posted by pamu
Code:
awk -F ";" '{for(i=1;i<=NF;i++){if($i ~ /chr|start|stop|symbol|gene_name|protein_name|info/){s=s?s";"$i:$i}}print s;s=""}' file

Dear Pamu,

Thanks a lot for your time.

I apologize for forgetting another small glitch in the input.

Between the chr, start and stop, there are two more columns.

I looked for unique names in those two columns and the second column has

Code:
HAVANA
ENSEMBL

The third column has

Code:
exon
CDS
start_codon
stop_codon

So, my input file is like this

Code:
chr1 HAVANA exon 100 200 + gene_name "alpha"; protein_name "alpha"; level 2; tag "basic"; info "known";
chr1 ENSEMBLE start_codon 245 290 + gene_name "alpha-1"; protein_name "alpha-2"; level 9; tag "basic"; info "uknown";
chr1 HAVANA CDS 310 320 + gene_name "alpha"; protein_name "alpha-4"; level 2; info "known";
chr1 ENSEMBLE stop_codon 355 490 + gene_name "alpha-1"; protein_name "alpha-120"; tag "basic"; info "valid";

Then my input becomes

Code:
chr1 HAVANA exon 100 200 + gene_name "alpha"; protein_name "alpha"; info "known";
chr1 ENSEMBLE start_codon 245 290 + gene_name "alpha-1"; protein_name "alpha-2"; info "uknown";
chr1 HAVANA CDS 310 320 + gene_name "alpha"; protein_name "alpha-4"; info "known";
chr1 ENSEMBLE stop_codon 355 490 + gene_name "alpha-1"; protein_name "alpha-120"; info "valid";

I edited the code with
Code:
[HAVANA:ENSEMBLE]

, but it didn't work.

I apologize for forgetting those two columns. Thanks again.
 

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