MetaPalette
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dkoslicki
Metagenomic profiling and phylogenetic distances via common kmers
wget http://files.cgrb.oregonstate.edu/Koslicki_Lab/MetaPalette/Bacteria.tar.gz fails for me. It says access forbidden. I would appreciate your guidance.
Hello, When I run MetaPalette on a even very small dummy dataset with precompiled Bacteria db, it ends with a "Segmentation fault (core dumped)". I tried both Docker version and...
As the title said - I ran Classify.py, only to find that one of my paths (to query_sequences) wasn't correct. Ctrl + C to interrupt seems to lead to an...
Is there a way to get an output that reports the taxonomy call of a contig rather than the overall % relative abundance of a taxa in the sample?
Calling classify.py e.g. with python Classify.py ... -Q \* ... breaks the code. Possible solution: re.escape(str(quality)) in classify.py, line 95ff.
I'm using the provided pre-trained data, with a test sample that has 2 million reads. It's a soil sample, so I would expect it to be diverse. I'm on a...
I have run the Classify.py program, but it does not produce the profile file which is needed for the next step. I have added the logging utility and trying to...
On some file systems, when reading thousands of files (from the training database) in parallel, every once in a while a file fails to open. Need to add error handling...
In the [formation of the hypothetical organism portion of the matrix](https://github.com/dkoslicki/MetaPalette/blob/master/src/Python/ClassifyPackage.py#L18-L32), a hypothetical column is added for each column of `A`, and for each `threshold`. Since the matrix `A` is...
It would be possible to traverse the training database once (in parallel) for many input samples. Currently, samples are classified one-by-one, and the training database is traversed each time. Could...