additional functionality when extracting random sequences

[avancise]

Hi,

I just stumbled across your package today while looking for a way to extract the same set of 10,000 1000kb loci randomly from five different genomes. Thank you so much for writing this package, I think it's going to be a huge help in this process. If you're still open to hearing requests for additional functionality/flexibility, I have two questions for you. For your function 'extract_random_seqs_from_genome', is it possible to set it so that replacement = FALSE once each random locus is selected and extracted (or is this already true)? Would it also be possible to set a minimum distance between randomly selected loci, e.g. if I wanted to specify that all loci are at least 50bp apart?

Thank you,
Amy

[HajkD]

Hi Amy,

Many thanks for contacting me and I am very happy to hear that you find metablastr useful!
I will try to take some time in the future to write some Vignettes to show the full scope of the package functionality.

Regarding your requests:

I just added the replace and prob arguments to extract_random_seqs_from_genome() so that you can specify it according to your needs. The default option is replace = TRUE.

I very much like your second request to draw random loci with a minimum distance to each other. Since this will require a more substantial amount of time to implement, I put it down as a feature request and will work on it as soon as I find some time for this.

Please feel free to add more ideas and requests and I will try my best to keep up with them :-)

Thank you so much!

Best wishes,
Hajk

[avancise]

Hi Hajk, Thank you so much for your quick reply! I appreciate you taking the time to add these functionalities, I think they will be very helpful (hopefully to others as well!). Just to make sure I understand correctly, if I add replace = FALSE to extract_random_seqs_from_genome(), the command will still hold replace = TRUE for the chromosome and strand to be sampled, but the 1kb sequence that was sampled will be removed? Or does adding replace = FALSE to the command affect all three of the sampling levels in the command? I thought of two other features that could be helpful as I was working today. If you are interested in either, should I submit them as feature requests? The first is an option to exclude sequences with too many Ns (for some that might be 1, for some that might be 10%, etc), and the second is an option to extract the same sequences from multiple fasta files. For now, I've written a python script to do the first, and am using your blast_genomes() command to find the extracted sequences in the rest of my fasta files. If you are interested in pursuing either of those, I can submit them as feature requests. Thank you again for your help and time! Your package has been very helpful already, and I've nearly got the random subset of sequences I need. Best, Amy

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On Thu, Sep 5, 2019 at 1:31 PM Hajk-Georg Drost ***@***.***> wrote: Hi Amy, Many thanks for contacting me and I am very happy to hear that you find metablastr useful! I will try to take some time in the future to write some Vignettes to show the full scope of the package functionality. Regarding your requests: I just added the replace and prob arguments to extract_random_seqs_from_genome() so that you can specify it according to your needs. The default option is replace = TRUE. I very much like your second request to draw random loci with a minimum distance to each other. Since this will require a more substantial amount of time to implement, I put it down as a feature request and will work on it as soon as I find some time for this. Please feel free to add more ideas and requests and I will try my best to keep up with them :-) Thank you so much! Best wishes, Hajk — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADZISFF5NUH26FSLB2OFTSDQIE7A3ANCNFSM4IUAHMYQ> .

[HajkD]

Hi Amy,

Thank you so much for your detailed response and I would be truly grateful if
if you could add these feature requests as a separate issue. I very much like all of these ideas and I am happy to add them to metablastr.

Just to confirm your question:

Just to make sure I understand correctly if I add replace = FALSE to
extract_random_seqs_from_genome(), the command will still hold replace = TRUE for the chromosome and strand to be sampled, but the 1kb sequence that
was sampled will be removed?

Initially, I also passed the replace argument to the chromosome and strand sampling, but
I now changed this and adapted it to your upper request. So yes, now the command will still hold replace =TRUE for the chromosome and strand to be sampled, but the 1kb sequence that was sampled will be removed :-)

Or does adding replace = FALSE to the command
affect all three of the sampling levels in the command?

Not anymore. But please let me know if you would find this functionality useful as well.

I hope this helps?

Thank you very much for all your help with this and for contributing these super useful ideas!

Best,
Hajk

[avancise]

Hi again Hajk,

Thank you again! This edit to the functionality of replace = TRUE in extract_random_seqs_from_genome() seems perfect to me. I submitted two new feature requests for the options I mentioned above. Let me know if I can do anything else, and thank you for working on these enhancements!

Best,
Amy

[HajkD]

Hi Amy,

I am very happy that it works for you now and thank you very much for opening the other feature requests :-)

I will start working on them once I find a bit of spare time.

Many thanks,
Hajk