pangenome - Create a diagram venn

Question

[BATMAN]

Hello, I would like to know if you can help me. I want to make a venn diagram with the presence and absence data (.Rtab) of roary (example fragment, the real list is about 8000 genes):

Gene    StrainA StrainB StrainC
group_633   1   0   1
group_644   1   0   1
group_669   1   0   1
ybeZ    1   1   1
maeB    1   1   1
smc_4   1   0   1
cas4-cas1   1   1   1
group_813   0   1   1
group_844   1   1   1
group_854   1   0   0
group_45    0   0   0
group_124   0   0   1
group_323   0   1   0

How can I delete the rows where the following pattern appears?

name 0 0 0

For Venn diagram:

The core gene is:

name 1 1 1

Accessory a+b:

name 1 1 0

Accessory b+c:

name 0 1 1

Accessories a+c:

name 1 0 1

unique a:

name 1 0 0

unique b:

name 0 1 0

unique c:

name 0 0 1

Thanks

Answer 1

[iraun]

As for your first question, how to delete rows with zero values, assuming that you have three columns with values as in your example, you can use the following awk command:

awk -F'\t' '{z=0; for (i = 1 ; i <= NF ; i++) if ($i == 0) z++} z < 3' input.tsv > output.tsv

If you have more than three value columns, replace z < 3 by. 4, 5, etc.

As for creating the venn diagram, I will separate the columns into different files with :

awk -F'\t' '$2 == 1 {print $1}' test.tsv > StrainA.tsv
awk -F'\t' '$3 == 1 {print $1}' test.tsv > StrainB.tsv
awk -F'\t' '$4 == 1 {print $1}' test.tsv > StrainC.tsv

And then use your venn diagram tool of interest with those three files, for example venny.