David Koslicki

Currently Associate Professor Of Computer Science and Engineering at Penn State University # Contributing to CSrankings Thanks for contributing to CSrankings! Here are some guidelines to getting your pull request...

Single character prefixes returning null prefix matches

1

For example, I have a `trie` with: ```python >>>list(tree.iterkeys("GC")) ['GCGx0x0'] ``` and yet: ```python >>>list(tree.iterkeys("G")) [] ``` `G` is certainly a prefix of `GCGx0x0`, so shouldn't it return the same...

Khmer (specifically `reverse_complement`) only intended for upper-case sequences?

2

Many reference FASTA/Q files have upper/lower case characters due to masking of low complexity sequences (like [here](https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#masking-of-low-complexity-sequences) or [here](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/dustmasker/)). I've noticed that: ```python >>>import khmer >>>khmer.reverse_complement("c") 'c' ``` yet ```python...

For the ``Read`` class, it appears that the ``sequence`` attribute is inaccessible when passed to a parallel pool. As a MWE, consider: ```python import multiprocessing import khmer def my_func(record): return...

n_unique_kmers() returns 0 upon save/reload

5

I noticed that using the Nodegraph method ``n_unique_kmers()`` returns 0 whenever a Nodegraph is saved and then reloaded. Minimum working example: ```python import khmer import tempfile import os temp_file =...

Bioconda version?

4

Given many cluster environments don't play well with Docker, are there any plans to put CAMISIM on Bioconda? @abremges @AlphaSquad @alicemchardy I have a student who can assist with this...

Per Alice's suggestion, try adding the mean (1/2)L1 error to the absolute performance plots

Due to changes in 428cd05, the old default of setting all branch lengths to 1 resulted in things like the following. For this profile: ``` # Taxonomic Profiling Output @SampleID:CAMI_LOW_S001...

Free text info from DrugBank

6

DrugBank has a bunch of extra information on their website; stuff like mechanisms of action:  I'm wondering if: a) this information exists in some downloadable part of DrugBank...

Single Exon node with the name `Exon`

3

I might have mentioned it before, but there is only a single node with the category `biolink:Exon`: a node with the name `Exon`. I think either the ETL-ing of whatever...