singlem query doesn't accept hyphens in sequences

[ljmmm]

Hi Ben,

I ran singlem query to assess similarity of ribosomal proteins within a set of genomes:
singlem query --query_otu_table fcpu_genomes_otu.csv --db fcpu_genomes.db/ > fcpu_rp_self_query.tsv

The analysis looked to run OK, however I got the following message in stderr:
CFastaReader: Hyphens are invalid and will be ignored around line 48
CFastaReader: Hyphens are invalid and will be ignored around line 106
CFastaReader: Hyphens are invalid and will be ignored around line 138
etc.

The hyphens in my files were generated by singlem pipe (representing gaps in the alignments). However it seems CFastaReader doesn't read them. Is there a CFastaReader-friendly gap character that could be used instead of hyphen?

Thanks,
Louis.

[wwood]

hey, thanks for the report.

That error msg comes from blast itself. Does it result in query sequences not hitting themselves?

[ljmmm]

Hi Ben, Ah yes it does. I can see now that the query sequence has "---" whereas the hit sequence has "NNN", which gives a divergence value of 1 in a lot of cases. Should I simply use sed to replace hyphens with Ns? Also, what is the cutoff for divergence that singlem is using here? I am a little unsure of how to interpret these results. Thanks! Louis.

…

On Fri, Jun 16, 2017 at 3:40 PM, Ben J Woodcroft ***@***.***> wrote: hey, thanks for the report. That error msg comes from blast itself. Does it result in query sequences not hitting themselves? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AbGosCgA0fPMdXVG1KzezHjs6Oilapvoks5sEhU9gaJpZM4N8By3> .

[wwood]

The default cutoff is 4, but you can change that with a command line parameter.

For what you are doing, I would set the divergence to be high (say 15) and then analyse those results. I wouldn't bother replacing them with Ns. The only thing to do here is for me to replace hyphens in the singlem query code.

[ljmmm]

Ok, great I'll try that. Thanks Ben and enjoy your weekend! Louis.

…

On Fri, Jun 16, 2017 at 4:07 PM, Ben J Woodcroft ***@***.***> wrote: The default cutoff is 4, but you can change that with a command line parameter. For what you are doing, I would set the divergence to be high (say 15) and then analyse those results. I wouldn't bother replacing them with Ns. The only thing to do here is for me to replace hyphens in the singlem query code. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AbGosCp0bCI9_fRLRW8EmAzGh2qWEmX1ks5sEhuXgaJpZM4N8By3> .

[wwood]

I've updated the query code to report the correct divergence in 2139f93 and 2bf4183 so that issue will be fixed in the next version. BLAST no longer spews that warning either.

[wwood]

and enjoy your weekend also sir.

[wwood]

This is no longer an issue since BLAST is no longer used for querying singlem DBs.