Selecting fastas for sliding windows

Question

[gubrins]

Heys,

I am trying to create sliding windows out of a huge fasta for doing a phylogeny of those windows. I already broke apart my fasta files for each individual in windows and I have all that information in a unique file. In order to create different files (for each one of the windows) I am running this for loop:

for i in $(cat sliding_windows.txt);
do
grep -A1 $i better_sliding_windows_one_line.fa > $i.txt
done

where sliding_windows.txt is:

:1-1000000
:1000001-2000000
:2000001-3000000
:3000001-4000000

and where better_sliding_windows... is a file containing all my samples per windows:

sample_1_sliding:1-1000000
sample_1_sliding:1000001-2000000
sample_1_sliding:2000001-3000000
sample_1_sliding:3000001-4000000
sample_1_sliding:4000001-5000000

(All the examples are cut, I have way more samples and data)

When I do the for loop in order to create a file per sliding windows, the problem is that between the fasta file of one sample and the next one, it creates a new line with two --, which is giving me problems in later stages. If I look for them with grep, I can't find them, but they are there. How could I avoid them to appear or remove them?

Any help would be more than helpful, let me know if is everything clear. Thanks in advance!

Answer 1

[cpad0112]

try --no-group-separator along with grep. If that doesn't work you can use sed or awk to remove --. However, I would suggest you to use https://bioinf.shenwei.me/seqkit/usage/#sliding for creating fasta files from each window, instead of using a shell loop. You can control the step and window sizes.

[gubrins]

that did the trick!! Thank you very much!!