Wojtek Bażant
Wojtek Bażant
Discovered by accident. To reproduce: ``` from ete3 import NCBITaxa ncbi=NCBITaxa("refdb/taxa.sqlite") ncbi.get_topology([1]) ``` I am using: Python 3.6.9 [GCC 8.4.0] on linux ete3 version (3.1.2) and the taxonomy version that...
Nice project, I don't have a use case for it but I've read some of it to learn about how you wrote it. As an idea - please only consider...
I've been looking at a lineage "Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria", common in MicrobiomeDB data. We use DADA2 with 138_SSURef_NR99 version of Silva, which does not include human mitochondria. I've found a paper from...
I had a problem with kneaddata_bowtie2_discordant_pairs taking increasingly more memory based on the input size. I've tracked it down to this script having to re-order the alignment information, for which...
I have a file with reads formatted like: ``` @SRR3132037.1 1 length=142 AAGGCGGCTGTTGTTATGTTATCGGCTCCATGCGAAACAGCAAAATTATTACAGCCCAGCGCATGTTACTGGTTCGCCTGTACCAGTTAGCAGAAAGGCGCGACCGTGTAACAGACGTACCGCGCCCCATCGCTATTTATCT +SRR3132037.1 1 length=142 /EEEEEEAEE/EEAEAEEEEEEEEEEE/EEEEEEEE6EEEEEEEEAEEEEEAEEAAA/AEEEEEAEEEEEEE/EE/EEAAE/EEEEEEEEAEE//EEE
Solves https://github.com/biobakery/humann/issues/19 ## Summary of changes - Load in reactions database only at the end as it needs 2GB RAM - Reimplement `store.Alignments` and `store.Reads` to use sqlite3, a core...
Thank you for the new version of `humann`! I've noticed that its memory usage increases with the fastq file size, even though `bowtie2` and `diamond` use a fixed block size....
Add id to payload of get_item_by_id_query. It's nice to have consistent return objects. I had some code for retrieving items from a board, wanted to reuse it with the other...
Hi, thank you for this package, I'm finding it very useful! This is a feature request for supporting paging for retrieval of items. I have more data than can be...