Find_uniq_kmers problem

[vilperte]

Hi,

I noticed that the script find_uniq_kmers might have a problem when when dumping the uniq kmers to a txt file.

It uses the min_count and max_count from the analyze_histogram steps. However, the max and min parameters should be passed in the beginning of the code and not by the end.

Instead of

dump_cmd = [kmc_cmd + '_dump', kmc_db, out_path,
                '-ci' + str(min_count), '-cx' + str(max_count)]

It should be

dump_cmd = [kmc_cmd + '_dump', '-ci' + str(min_count), '-cx' + str(max_count), 
               kmc_db, out_path]

[esrice]

Hi, Thanks for the bug report. Are you actually getting an error, and if so, what is it? Also, what version of kmc are you using? This works as written with v3.2.1 (the current version in bioconda and the latest release on github), so all I can think of is that earlier versions might be less flexible with argument order. I'll look into it further if you can give me more details. Thanks!

…

On Tue, Aug 30, 2022, 11:11 AM vilperte ***@***.***> wrote: Hi, I noticed that the script find_uniq_kmers might have a problem when when dumping the uniq kmers to a txt file. It uses the min_count and max_count from the analyze_histogram steps. However, the max and min parameters should be passed in the beginning of the code and not by the end. Instead of dump_cmd = [kmc_cmd + '_dump', kmc_db, out_path, '-ci' + str(min_count), '-cx' + str(max_count)] It should be dump_cmd = [kmc_cmd + '_dump', '-ci' + str(min_count), '-cx' + str(max_count), kmc_db, out_path] — Reply to this email directly, view it on GitHub <#13>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLL5JJVOFE6OEEAIHAGXG3V3YQAPANCNFSM6AAAAAAQAQFWAQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[vilperte]

Thanks for the quick reply.

There is no error actually, but I was getting an uneven binning of my F1, so I tried to find what was happening.

I am indeed using an older version (v3.1.1), my fault for not checking before, sorry. But I tested now with v3.2.1 and passing the -ci and -cx parameters at the end of the command still outputs the full amount of kmers.

[esrice]

Oh, weird. Investigating now. Thanks for bringing this to my attention.

[esrice]

Oh, weird. I'll fix this tomorrow, or feel free to submit a PR. Thanks for noticing.

…

On Tue, Aug 30, 2022, 12:36 PM vilperte ***@***.***> wrote: Thanks for the quick reply. There is no error actually, but I was getting an uneven binning of my F1, so I tried to find what was happening. I am indeed using an older version (v3.1.1), my fault for not checking before, sorry. But I tested now with v3.2.1 and passing the -ci and -cx parameters at the end of the command still outputs the full amount of kmers. — Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLL5JLHM65QABCPDMP7N4DV3Y2BBANCNFSM6AAAAAAQAQFWAQ> . You are receiving this because you commented.Message ID: ***@***.***>