asztandi

Yes, that would be the ideal scenario, having the MAF file and the index side-by-side on the FTP server.

Using a BigMaf file would be great. Maybe I missed it but I couldn't find a way to randomly search for a region using a Bigmaf file, something similar to...

Looked into working with a BigMaf file. Both parsing ``` alignments = BioAlign.parse(bigmaf_file, "bigmaf") ``` followed by searching ``` sel_aligns = alignments.search(anchor_seq_name, start, end) for a in sel_aligns: ``` is...

Thank you for the explanation regarding the exception. > Do you have some timings? Yes, please find them below. Method A ``` idx = MafIO.MafIndex(index_file, maf_file, anchor_seq_name) alignments = idx.search([start],...

> When I try this on the multiz100way multiple genome alignments from UCSC for chrY, I am getting 0.011 seconds for the bigMaf file I see the exact same speed...

Yes, please take a look at: https://ftp.ncbi.nlm.nih.gov/comparative-genome-viewer/mcgv/43_mammals_epo/filtered/ The bigMaf is the 43_mammals.epo.1_filtered.bb This is for chromosome 1. The MAF file for chr Y is 43_mammals.epo.Y_filtered.maf

Thank you so much for all your suggestions. We will incorporate them in our bigMaf workflow. After we search for a specific region (that may be within one MAF block...

Thank you @mdehoon for all the timing details! I also noticed, as you mentioned in your comment, that obtaining one alignment is much slower using Method B. That was another...