Comments (5)
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
from metablastr.
from metablastr.
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 holdreplace = 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
from metablastr.
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
from metablastr.
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
from metablastr.
Related Issues (12)
- blast_best_reciprocal_hit nucleotide-protein comparison task error HOT 1
- Error: Internal error in `dict_hash_with()`: Dictionary is full.
- How can I load sequences from a CSV file and do the massive Blast search locally?
- Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : cannot open file '' HOT 2
- Package release request HOT 2
- blast_nt for nucleotide against NCBI database HOT 3
- Feature Request: exclude sequences with Ns
- Feature Request: extract the same regions from multiple samples
- function blast_protein_to_protein with argument is.subject.db = TRUE doesn't work with nr database HOT 5
- Feature request : add taxon id for each blast hit HOT 3
- Reg: Reciprocal hits from already run blast outcomes HOT 5
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from metablastr.