[SOLVED] Extract text from file in Linux: specific line; between 2 different patterns

Issue

I have a bunch of text files, all with the same structure, and I need to extract a specific piece in a specific line.

I can easily extract the line with awk:

awk 'NR==23' blast_out.txt

CP046310.1 Lactobacillus jensenii strain FDAARGOS_749 chromosome,...  787     0.0 

But I don't want the whole line, rather just the part between the first space on the left (after CP046310.1) and the double space on the right (before 787). The final output should be:

Lactobacillus jensenii strain FDAARGOS_749 chromosome,...

I tried several combination of awk and grep but cannot find the correct one to extract this specific pattern.

Solution

1st solution: With your shown samples, please try following awk code. Simple explanation would be, nullifying 1st, 2nd last field and last field, then globally substituting starting and ending space with NULL, then printing the line.

awk '{$1=$NF=$(NF-1)="";gsub(/^ +| +$/,"")} 1' Input_file

OR to run it on 23rd line change it to:

awk 'FNR==23{$1=$NF=$(NF-1)="";gsub(/^ +| +$/,"");print;exit}' Input_file

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2nd solution: Going through fields and printing values which are required as per need.

awk '{for(i=2;i<(NF-1);i++){printf("%s%s",$i,i==(NF-2)?ORS:OFS)}}' Input_file

OR on 23rd line try following:

awk 'FNR==23{for(i=2;i<(NF-1);i++){printf("%s%s",$i,i==(NF-2)?ORS:OFS)};exit}' Input_file

Answered By - RavinderSingh13

Answer Checked By - Cary Denson (WPSolving Admin)