I have 2 text file which I want to merge them in a new file.
my first file is look like
DjScaffold1002 blastx protein_match 50305 51044 125 - . ID=DjScaffold1002:hit:2832:3.10.0.0;Name=sp|Q9UEW3|MARCO_HUMAN DjScaffold1002 blastx protein_match 50305 50892 208 - . ID=DjScaffold1002:hit:2833:3.10.0.0;Name=sp|Q60754|MARCO_MOUSE DjScaffold1002 blastx protein_match 44584 45176 145 - . ID=DjScaffold1002:hit:2834:3.10.0.0;Name=sp|Q7SIB2|CO4A1_BOVIN
and second file =
Q9UEW3 MARCO Q60754 Marco Q7SIB2 COL4A1
and my expected output like, I mean mapping part of 9th column string from first line with 1st column of second file, should be like :
DjScaffold1002 blastx protein_match 50305 51044 125 - . ID=DjScaffold1002:hit:2832:3.10.0.0;Name=sp|Q9UEW3|MARCO_HUMAN;Symbol=MARCO DjScaffold1002 blastx protein_match 50305 50892 208 - . ID=DjScaffold1002:hit:2833:3.10.0.0;Name=sp|Q60754|MARCO_MOUSE;Symbol=Marco DjScaffold1002 blastx protein_match 44584 45176 145 - . ID=DjScaffold1002:hit:2834:3.10.0.0;Name=sp|Q7SIB2|CO4A1_BOVIN;Symbol=COL4A1
Also, I wanted to keep line from first file which were not mapped with second file.
How can perform that with awk?
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Answer
You can use awk to merge them:
awk 'FNR == NR{a[$1]=$2; next} $2 in a{$0 = $0 ";symbol=" a[$2]} 1' f2 FS='[|]' f1
L1 code=c|id1|;name=name1;symbol=symbol1
L2 code=c|id2|;name=name1;symbol=symbol2
L0 code=c|id0|;name=name0;
For your edited samples:
awk 'FNR == NR{a[$1]=$2; next} $2 in a{$0 = $0 ";symbol=" a[$2]} 1' f2 FS='[|]' f1
DjScaffold1002 blastx protein_match 50305 51044 125 - . ID=DjScaffold1002:hit:2832:3.10.0.0;Name=sp|Q9UEW3|MARCO_HUMAN;symbol=MARCO
DjScaffold1002 blastx protein_match 50305 50892 208 - . ID=DjScaffold1002:hit:2833:3.10.0.0;Name=sp|Q60754|MARCO_MOUSE;symbol=Marco
DjScaffold1002 blastx protein_match 44584 45176 145 - . ID=DjScaffold1002:hit:2834:3.10.0.0;Name=sp|Q7SIB2|CO4A1_BOVIN;symbol=COL4A1