bioutils

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Cribbing description from https://github.com/biocommons/hgvs/pull/737 > A lot of modern editors will auto-trim trailing whitespace upon save. Unfortunately, if there's a pesky space or two hanging around on some old file,...

jsstevenson

Ensembl transcript ENST00000617537.5 sequence is genomic not cdna

9

https://asia.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000136250;r=7:36512941-36724494;t=ENST00000617537 Web page Reports that the sequence is 2385 bases long Ensembl API is in agreement: ``` In [25]: import requests In [26]: url = "https://rest.ensembl.org/sequence/id/ENST00000617537?type=cdna" In [27]: r =...

davmlaw

Stop pinning urllib3 (only done for testing dep)

4

This fixes a problem where one cannot install `bioutils` into an environment where `urllib3` version 2 is being used. In other words, merely installing `bioutils` forces you to use `urllib3`...

DavidCain

The [Human Mitochondrial codon](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) table includes the alternate initiator codon ATT. The correct translation of the first three codons in [MT-ND2](https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1) should be `MNP`. But the translate_cds method in the...

bsgiles73