The command of Methphaser N50

[Humonex]

We noticed that your N50 is different from Whatshap N50, and the Methphaser N50 is more reasonable. Could you please provide a command to call the N50 calculation method in the code or provide a script to calculate N50?
for example the code in the [post_processing_script.ipynb]
get_methphase_n50(block_relationships_df_30x_high_acc),
get_methphase_n50(block_relationships_df_60x_high_acc),
get_methphase_n50(block_relationships_df_LSK60x_high_acc),
get_methphase_n50(block_relationships_df_LSK30x_high_acc),
get_methphase_n50(block_relationships_df_80x_high_acc)
or the code in the file [meth_phaser_post_processing]
def get_n50(final_block_dict):
chrom_n50 = {}
for chrom in final_block_dict.keys():
block_len_list = []
for i in final_block_dict[chrom]:
block_len_list.append(i[1] - i[0])
sum_block_len = 0
for i in sorted(block_len_list, reverse=False):
sum_block_len += i
if sum_block_len > sum(block_len_list) / 2:
chrom_n50.update({chrom: i})
break
return chrom_n50
But it seems that this function has not been called.

[Fu-Yilei]

get_genome_n50

should be this one I guess. Forgot the details.

[Humonex]

Yes, I have seen the get_genome_n50 in the [post_processing_script.ipynb], do I need to fully run this .ipynb every time if want to get the Methphaser N50?

[Fu-Yilei]

Not really. I think it takes the middle csv files as input.

[Humonex]

Thank you, I know this, I think it would be more convenient for people to use the software and promote the popularity of Methphaser N50 if the get_genome_n50 could be added to [methphasing] or have a command to call the function.