Update whale-watch.py

[dhoconno]

I think recent file format changes can cause whale-watch.py to fail. I was able to fix with two tweaks:

Line 30: change 'fastq' to 'filename_fastq'

Line 52: add 'skiprows=6,' to skip header in PAF file.

Cheers,

dave

[alexomics]

Hi Dave,

The filename field is not actually used so can safely be removed from the list on line 31. I have made this change in the develop branch (commit 64229af). If you could test this with your dataset, that would be very helpful.

As for reading in the PAF file, the PAF format doesn't specify a header row or rows. So this would lead to inadvertently excluding mappings from the script; therefore I have not included this change.

What command are you using to generate your mappings? We use:

$ minimap2 -x map-ont reference.mmi *.fastq > mappings.paf

Please let me know how these work for you.

Alex

[dhoconno]

Hi Alex,

I'm mapping with a command similar to yours. But the top six rows look like headers, but it might actually be stderr content that is getting saved to my output file?

[M::mm_idx_gen::512.939*0.70] collected minimizers
[M::mm_idx_gen::591.117*0.72] sorted minimizers
[M::main::591.117*0.72] loaded/built the index for 195 target sequence(s)
[M::mm_mapopt_update::595.799*0.72] mid_occ = 694
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 195
[M::mm_idx_stat::597.579*0.72] distinct minimizers: 100167746 (38.80% are singletons); average occurrences: 5.519; average spacing: 5.607
11780e2c-77e3-42d3-b884-57d468156989    201     95      151     -       chr12   133275309       23630798        23630852        40      56      0       tp:A:P  cm:i:3  s1:i:40 s2:i:0  dv:f:0.0732     rl:i:0
c0a137db-7c95-4d12-aeb2-9871670baf0f    220     120     212     -       chr4    190214555       155116878       155116975       45      97      1       tp:A:P  cm:i:3  s1:i:44 s2:i:0  dv:f:0.0803     rl:i:122
c898b165-6b77-4100-aff1-1a77f9f8a071    271     49      140     -       chr11   135086622       15677644        15677735        58      91      29      tp:A:P  cm:i:6  s1:i:58 s2:i:0  dv:f:0.0835     rl:i:0
2cd0ee94-57da-46b8-ad86-07d0c5538d71    493     53      267     -       chr11   135086622       73953443        73953652        87      215     10      tp:A:P  cm:i:9  s1:i:87 s2:i:81 dv:f:0.0978     rl:i:0

This isn't a big deal, though. I have another issue but will start a separate ticket.