How to extract sequences from multiple fasta files according to my list files

Question

[sohjiro4321]

I have done orthologous analysis in four fasta files from four different species. After orthologous analysis, I obtain orthologous gene list. For example: orthologous gene 1: 1st species (gene_id1), 2nd species (gene_id2), 3rd species (gene_id3), 4th species (gene_id4) orthologous gene 2: 1st species (gene_id1'), 2nd species (gene_id2'), 3rd species (gene_id3'), 4th species (gene_id4') ......

I would like to extract sequences from each fasta files from different species and put them into separate fasta files according to list. How could I perform these requests?

Answer 1

[EVR]

seqtk subseq -l 100000 input.fasta gene_list.txt

[sohjiro4321]

thank you for providing information. May I ask a further question? Would there be specific format in gene_list.txt? And by the way, I have four input.fasta. How do I extract orthologous sequences from four independent fasta into each orthologous gene fasta files?

[EVR]

gene_list.txt

gene_id1 gene_id2 gene_id3

Use the above command separately for every fasta file you have