how to find mismatch pattern from one file to another

Question

[Kumar]

I have two tab delimited files, one contains list of nodes (file 1) and another file contains list of nodes and its additional details. I need to find nodes (file 1), which are not matching in another file (file 2). Please see example below:

File 1:
NODE_35_length_25224_cov_45.741
NODE_42_length_28456_cov_53.6579
NODE_43_length_25224_cov_33.7544
NODE_226_length_737_cov_1.98094

File 2:
NODE_35_length_25224_cov_45.741 Prodigal:2.6    CDS 58  777 .   -   0   ID=LGE0470
NODE_42_length_28456_cov_53.6579    Prodigal:2.6    CDS 58  777 .   -   0   ID=LGE0445

OUTPUT:
NODE_43_length_25224_cov_33.7544
NODE_226_length_737_cov_1.98094

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[cpad0112]

with tsv-utils:

$ tsv-join --e --f file2.txt --k 1 file1.txt 
NODE_43_length_25224_cov_33.7544
NODE_226_length_737_cov_1.98094

Answer 1

[ATpoint]

grep -vf <(awk -F "\t" '{print $1}' file2) file1

Try to understand what the function does. The core part is grep -v -f, many tutorial on grep out there.

[Kumar]

This command taking too long time without any output. My files are tab delimited..

[Mensur Dlakic]

My files are tab delimited..

Instead of -F " ", try -F "\t".

[ATpoint]

Changed delimiter in my comment.

[ATpoint]

Try to understand why, otherwise it is impossible to debug, especially when commands get more complex.

Answer 2

[cpad0112]

you can use simpler one:

$ cut -f 1 file2.txt  | grep -vf - file1.txt 
NODE_43_length_25224_cov_33.7544
NODE_226_length_737_cov_1.98094

or using only awk :

$ awk -F "\t" 'NR==FNR{a[$1];next} !($1 in a)' file2.txt file1.txt
NODE_43_length_25224_cov_33.7544
NODE_226_length_737_cov_1.98094