bioinfo | NeVOmics | Genomics library

I have properties as below;

In these slides (13) the deletion of a point in a kd-tree is described: It states that the left subtree can be swapped to be the right subtree, if the deleted node has only a left subtree. Then the minimum can be found and recursively be deleted (just as with a right subtree).

This is because kd-trees with equal keys for the current dimensions should be on the right.

My question: Why does the equal key point have to be the right children of the parent point? Also, what happens if my kd-tree algorithm returns a tree with an equal key point on the left?

For example: Assume the dataset (7,2), (7,4), (9,6) The resulting kd-tree would be (sorted with respect to one axis):

I want to automate the web-server http://bioinfo.unipune.ac.in/IRESPred/IRESPred.html using python selenium.

I recently upgraded my MacOSX system to Catalina and several files were placed automatically into "Relocated items" folder on my Desktop. I recently tried to run the following code which had previously worked:

The pseudo-code for nearest neighbor (NN) search in Wikipedia is not tractable enough for me. Few more posts available with implementations, but they seem to be language specific. So I'm finding it hard to understand how NN search works. This diagram is taken from https://www.cs.cmu.edu/~ckingsf/bioinfo-lectures/kdtrees.pdf. And I'm trying to understand it with a specific case say query point Q = (52,52). Assume two dim are (x,y) and root level splits by x-dim.

Searching NN:

First, I go down from root to a leaf as if I'm trying to insert the Q; and doing so, the leaf is (55,1). Update a (global) var current_best from INFINITY to (55-52)² + (1-52)² = 2610.

Next, I go up to (70,70) and updates current_best from 2610 to 18²+18²=648. Since this gives better distance, we must probe it's sub-tree: is this correct understanding?

Further, we see node (60,80) doesn't give better result (i.e. no update for current_best).

In the process of going up further, we find root (51,75) gives even better result (current_best gets set to 530). So, applying my understanding, we must check it's other sub-tree.

The (25,40) doesn't yield any better result. What I understand is that we still need to verify the sub-tree of (25,40). However, in this case, since this node uses y-dim, and since Q.y > 40, we need to check only right sub-tree (rooted at (35,90)): is this correct understanding?

In short, what I see is if a node provides better result for current_distance, we must probe both children nodes; and if a node does NOT provide better result, all we can do it ignore one of the sub-tree but must probe the other sub-tree based on the condition (splitting hyperplane by specific dimension). Is this correct understanding?

Finally, I'll really appreciate anyone providing a tractable pseudo-code for NN search for Kd-tree

I have this following regex:

/<(?:textarea|select)[\s\S]*?>[\s\S]*?(\{\{\{variable:(.+?)\}\}\})[\s\S]*?<\/(?:textarea|select)>|<(?:input)[\s\S]+?(value=[\s\S]+?)(\{\{\{variable:(.+?)\}\}\})[\s\S]+?>|(\{\{\{variable:(.+?)\}\}\})/im

And this (shortened) HTML document:

I'm packaging some common functions in a small Perl module, that I load in the script using

After installing PlasmidSeeker on LinuxMint19, I cannot run its Perl script

It is always "Permission denied" although I've given all the permissions to plasmidseeker.pl

I'm using R 3.4.1 on Red Hat Enterprise Linux 6. I have version 3.0 of package asreml installed under /tools/bioinfo/app/R-3.4.1/lib64/R/library.