eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Fix yeast genome #225

Closed eweitz closed 4 years ago

eweitz commented 4 years ago

This fixes Ideogram handling for baker's yeast, Saccharomyces cerevisiae. The problem was reported by @vsoch in #223.

The break seems to have been caused by an NCBI database, either Taxonomy or Assembly (or one their E-Utils interfaces), changing its taxon object for the search term "saccharomyces cerevisiae" or the organism's representative genome. Searching Taxonomy via E-utils for that term returns a species-rank taxon (taxid 4932). However, the Assembly record is for a strain-rank taxon (taxid 559292). The mismatch broke Ideogram for yeast.

It seems there was also a separate, lurking bug in chromosome ordering in Ideogram.js. Yeast chromosomes are labeled using Roman numerals. "Natural" sort coincidentally handles such genomes with few chromosomes (as in C. elegans, with chromosomes I through V, X and MT). But natural sort fails beginning at Roman numeral 9 (IX), and yeast has 16 chromosomes. Yeast chromosomes were not only newly missing, but also likely always had been misordered.

This change:

Here is the yeast genome in Ideogram:

ideogram_yeast_genome
coveralls commented 4 years ago

Coverage Status

Coverage increased (+0.1%) to 89.68% when pulling 3b42aba83c3e4bcd541a72402214055a728a39c5 on fix-yeast into a073a3acbaa31adb732a722077f3785495a78ce3 on master.