Incorrect display in metagenotype display names

[jseager7]

The latest update to the website has caused problems with the metagenotype display names on the gene pages. Using PHIG:277 as an example:

The pathogen name Hyaloperonospora arabidopsidis is missing, the strain names are missing, and the host genotype is followed by the text "(null)".

Here's how the metagenotype name should be displayed in this case:

ATR1-delta51 (partial_amino_acid_deletion) [Not assayed] H. arabidopsidis (Emoy2) RPP1-TIRE158A (amino_acid_mutation) [Not assayed] A. thaliana (ecotype Wassilewskija-0)

The same problem happens for wild-type hosts:

We expected to see this:

TRI5+ (wild_type) [Wild type product level] F. graminearum (PH-1) wild type T. aestivum (cv. Bobwhite)

And on some pages, there are empty parentheses instead of the text "(null)". PHIG:348 is one example:

The host name is missing here too. We expected to see this:

3LysMdelta (deletion) Z. tritici (IPO323) CEBip silenced (other) [Knockdown] T. aestivum (cv. Riband)

[jseager7]

Note that in my original comment I forgot to mention that the strain names are missing from the metagenotype display names too. I've updated the comment now.

[jseager7]

This seems to be fixed for PHIG:277 but I'm still noticing problems for other genes, such as PHIG:279.

The host genotype is missing its species name and strain name, only one of the three alleles in the genotype are shown, and the expression level is not enclosed in square brackets. I expected to see this:

FER1(a genome) (wild type) [Knockdown] FER1(b genome) (wild type) [Knockdown] FER1(d genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite)

[jseager7]

@jashobanta-mcpl The display seems to be fixed on the current version of the website, as shown below:

However, in today's meeting, it seemed like the host species and strain was being repeated after every host allele, instead of being shown only once at the end of the host genotype display name. For exmaple:

FER1(a genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER1(b genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER1(d genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER2(a genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER2(b genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER2(d genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite)

Shown with line breaks for clarity:

FER1(a genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER1(b genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER1(d genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER2(a genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER2(b genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite) FER2(d genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite)

We only want the host species and strain name to be shown once, at the end of the display name, since the other alleles will always be from the same species and strain and therefore the rest of the information is redundant.

Here's how the display name should be shown, without line breaks:

FER1(a genome) (wild type) [Knockdown] FER1(b genome) (wild type) [Knockdown] FER1(d genome) (wild type) [Knockdown] FER2(a genome) (wild type) [Knockdown] FER2(b genome) (wild type) [Knockdown] FER2(d genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite)

Again, with line breaks for clarity:

FER1(a genome) (wild type) [Knockdown] FER1(b genome) (wild type) [Knockdown] FER1(d genome) (wild type) [Knockdown] FER2(a genome) (wild type) [Knockdown] FER2(b genome) (wild type) [Knockdown] FER2(d genome) (wild type) [Knockdown] T. aestivum (cv. Bobwhite)

[CuzickA]

https://poc.molecularconnections.com/phibase-v3/#/search-detail-page/PHIG:253

I think we want to omit the brackets in '(wild type)' in front to the T. aestivum when it is a host with no specified genes. The metagenotype should look like the text recorded above

[jseager7]

The use of "(wild type)" for wild type host genotypes is a regression, since it was shown without brackets in a previous version of the display.

See https://github.com/PHI-base/PHI5_web_display/issues/69#issue-1459897922

[jashobanta-mcpl]

wild type - bracket issue is fixed .

[jseager7]

@jashobanta-mcpl Thanks, the display of wild type hosts is now correct on all the gene pages I've checked. The rest of the metagenotype display seems correct too.