Feature: Output Pangenome sequence

[josiahseaman]

Would you be so kind as to modify ODGI bin at 1bp bins to output a pangenome sequence? It'd be the concatenation of all node sequences in the order that you already sorted them. A single long string.

#Python pseudocode for pangenome matrix sequence
with open(bin_output_file, 'w') as out:
	out.write(regular_bin_output(my_sort_order))
	if bin_size == 1:
		out.write("'Pangenome Sequence':")
		pangenome = ''.join(node.seq for node in my_sort_order)
		out.write(pangenome)

This could potentially be triggered at every bin level or only bin_size = 1bp. Sequence length with real data tend to be 120% the size of the starting genome, so 100s of MB, not 100s of GB. Perhaps a command line flag? --emit_sequence

[ekg]

I think this should be the default behavior. I can make that so it ends up in the bin output.

…

On Tue, Oct 8, 2019 at 5:11 PM Josiah Seaman ***@***.***> wrote: Would you be so kind as to modify ODGI bin at 1bp bins to output a pangenome sequence? It'd be the concatenation of all node sequences in the order that you already sorted them. A single long string. #Python pseudocode for pangenome matrix sequencewith open(bin_output_file, 'w') as out: out.write(regular_bin_output(my_sort_order)) if bin_size == 1: out.write("'Pangenome Sequence':") pangenome = ''.join(node.seq for node in my_sort_order) out.write(pangenome) This could potentially be triggered at every bin level or only bin_size = 1bp. Sequence length with real data tend to be 120% the size of the starting genome, so 100s of MB, not 100s of GB. Perhaps a command line flag? --emit_sequence — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#49>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABDQEPASZCWM76BHAJLYPTQNSPIPANCNFSM4I6TC2VQ> .