Samtools and fax, deal with strand

Question

[Darrill]

Hi everyone one, I have a tab file such as :

seqnames start end  strand
1 scaffold_0 1 50 -
2 scaffold_0 30 120 +
3 scaffold_0 60 400 -
4 scaffold_0 100 300 +

and the idea I had was to use Samtools faidx to get all the fasta sequences in my genome from the coordinates start and end by first creating a get_fasta.txt file such as:

scaffold_0:1-50
scaffold_0:30-120
 scaffold_0:60-400
scaffold_0:100-300

and then use the commande /samtools faidx my_genome.fa get_fasta.txt

But as you can see, the coordinates are wrong for the strand - and should be replaced by :

seqnames start end  strand
1 scaffold_0 50 1 -
2 scaffold_0 30 120 +
3 scaffold_0 400 60 -
4 scaffold_0 100 300 +

So my question is:

Do you know if samtools can deal with strand and automatically pars the column strand in order to take the good coordinates?

Thank you for your help.

[Pierre Lindenbaum]

how about using https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ?