How to split big .faa file into smaller .faa files

Question

[Shaurya]

I have a 10 gb .faa proteomes file that I want to run MAFFT on. But it is too big and hence I need to divide the file. How do I convert it to smaller files in windows without losing any data ? The solutions I have come across are for a UNIX/LINUX based environment

[cpad0112]

from the statement The solutions I have come across are for a UNIX/LINUX based environment, I am assuming that you are on windows. Even in windows (=>10), you can use GNU-linux tools using wsl2. I would suggest seqkit (windows version) from here. Please go through the manual and there are multiple ways to split a fasta using seqkit in manual.

Answer 1

[Mark]

Seqkit is the answer.

To split into 100 parts:

seqkit split myfile.faa --by-part 100

To split by number of desired sequences per file (eg 5000 per file):

seqkit split myfile.faa --by-part 5000 -by-size

The solutions I have come across are for a UNIX/LINUX based environment

Yes, use linux, if you want to perform any bioinformatics you need to use linux

Answer 2

[Divon]

You can use my Genozip tool:

genozip myfile.faa
genocat --downsample 3,1 myfile.faa.genozip   <--- get part 1 out of 3

Works on Windows (as well as Linux and Mac)

See here: https://genozip.com/downsampling.html

Paper: https://www.researchgate.net/publication/349347156_Genozip_-_A_Universal_Extensible_Genomic_Data_Compressor

Answer 3

[Juke34]

14 methods reviewed here: https://github.com/Juke34/knowledge/blob/main/split_fasta.md