Some of the annotation qualifiers can be displayed as HTML hyperlinks:

To complement the command add qualifier_link, we now have the command edit qualifier_link. If you want to modify the link's URL or use another qualifier that will supply the value for the link, edit the corresponding record. In the example below, we will change "http" to "https" in the link that will incorporate the value of qualifier Name into the URL:

PS> edit qualifier_link "Glycine (genus)/Glycine max/Wm82.a4.v1"
Qualifier links (qualifier name and URL) for /Glycine (genus)/Glycine max/Wm82.a4.v1:
[0]     Name          http://phytozome-next.jgi.doe.gov/report/transcript/Gmax_Wm82_a4_v1/%s
[1]     KOG           https://www.ncbi.nlm.nih.gov/Structure/cdd/%s
[2]     Pfam          http://pfam.xfam.org/family/%s
[3]     Panther       http://www.pantherdb.org/panther/familyList.do?searchType=basic&fieldName=all&organism=all&listType=6&fieldValue=%s
[4]     KO            https://www.genome.jp/dbget-bin/www_bget?%s
[5]     GO            https://www.ebi.ac.uk/QuickGO/term/%s
[6]     Transcript    https://www.ncbi.nlm.nih.gov/nuccore/%s

Please enter line [number] for the qualifier link to edit (delete): 0
Qualifier name (make it blank to delete)? Name
URL template? https://phytozome-next.jgi.doe.gov/report/transcript/Gmax_Wm82_a4_v1/%s

Qualifier name: Name
URL template: https://phytozome-next.jgi.doe.gov/report/transcript/Gmax_Wm82_a4_v1/%s
MapSetId: 34
Do you want to save the modified qualifier link? (Y/N) Y
1 qualifier link has been modified

Note, that this command will allow deleting the qualifier links. Just change the name of the corresponding qualifier to an empty string.


PS> edit qualifier_link "Glycine (genus)/Glycine max/Wm82.a4.v1"
Qualifier links (qualifier name and URL) for /Glycine (genus)/Glycine max/Wm82.a4.v1:
[0]     Name          https://phytozome-next.jgi.doe.gov/report/transcript/Gmax_Wm82_a4_v1/%s
[1]     KOG           https://www.ncbi.nlm.nih.gov/Structure/cdd/%s
[2]     Pfam          http://pfam.xfam.org/family/%s
[3]     Panther       http://www.pantherdb.org/panther/familyList.do?searchType=basic&fieldName=all&organism=all&listType=6&fieldValue=%s
[4]     KO            https://www.genome.jp/dbget-bin/www_bget?%s
[5]     GO            https://www.ebi.ac.uk/QuickGO/term/%s
[6]     Transcript    https://www.ncbi.nlm.nih.gov/nuccore/%s

Please enter line [number] for the qualifier link to edit (delete): 6
Qualifier name (make it blank to delete)? Erase the qualifier name here to delete
Do you want to remove the qualifier link for Transcript? (Y/N) Y
1 qualifier link has been deleted

Using regular expressions to extract substrings and convert them into hyper-links

A qualifier value (such as Dbxref) can contain multiple identifiers. Use regular expressions to extract the substrings used later as part of the hyper-links.