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:
Adds a manual copy of chromosome data from yeast genome assembly R64 (sarCer3, GCA_000146045.2)
Fixes sorting for chromosomes with Roman numerals as names
Coverage increased (+0.1%) to 89.68% when pulling 3b42aba83c3e4bcd541a72402214055a728a39c5 on fix-yeast into a073a3acbaa31adb732a722077f3785495a78ce3 on master.
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: