Ann Loraine added a comment - 21/May/24 9:45 AM Request for Paige Kulzer : Please transfer your comment on what you would like to see done (from your email from yesterday or last week?)

Paige Kulzer added a comment - 21/May/24 9:49 AM Can we please add keywords such as "F3H" and "flavanone 3-hydroxylase" to the gene annotations labeled "PRAM_26184.1" in SL5 and "solyc02g083860" in SL4? This will allow me to quickly search for and locate the gene where the point mutation occurs in the are genotype.

Paige Kulzer added a comment - 22/May/24 9:24 AM Please fix the following spelling error: hydroxlase -> hydrox y lase

Ann Loraine added a comment - 26/May/24 12:14 PM - edited Annotation description change process: Update IGB quickload local copy to get most up-to-date version of the repository cd quickload svn up extract line for PRAM_26184.1 and save to a temp file gunzip -c S_lycopersicum_Jun_2022.bed.gz | grep PRAM_26184.1 > txt.bed Edit txt.bed to contain text we want to use instead: anthocyanin-reduced (are) flavanone 3-hydroxylase (F3H) SL4:Solyc02g083860 Create new bed file lacking info lacking line for F3H gene (will be replaced in future step): gunzip -c S_lycopersicum_Jun_2022.bed.gz | grep -v PRAM_26184.1 > S_lycopersicum_Jun_2022.bed Check it has the right number of lines: local aloraine$ gunzip -c S_lycopersicum_Jun_2022.bed.gz | wc -l 43752 local aloraine$ wc -l S_lycopersicum_Jun_2022.bed 43751 S_lycopersicum_Jun_2022.bed It's all good. Add new text to new file: cat txt.bed S_lycopersicum_Jun_2022.bed | sort -k1,1 -k2,2n | bgzip > S_lycopersicum_Jun_2022.bed.gz Check my work: gunzip -c S_lycopersicum_Jun_2022.bed.gz | diff - S_lycopersicum_Jun_2022.bed 17845d17844 < 2 47448952 47451152 PRAM_26184.1.p1 0 - 47449290 47451066 0 3 638,429,446, 0,706,1754, PRAM_26184 anthocyanin-reduced (are) flavanone 3-hydroxylase (F3H) SL4:solyc02g083860 The new file contains the newly crafted line for the gene. Create a new index: local aloraine$ tabix -s 1 -b 2 -e 3 S_lycopersicum_Jun_2022.bed.gz local aloraine$ New index is made. All is good. Added to the repository: local aloraine$ svn ci S_lycopersicum_Jun_2022.bed.gz S_lycopersicum_Jun_2022.bed.gz.tbi -m "IGBF-3712 Improve gene description for anthocyanin-reduced (are) in SL5" Sending S_lycopersicum_Jun_2022.bed.gz Sending S_lycopersicum_Jun_2022.bed.gz.tbi Transmitting file data ..done Committing transaction... Committed revision 189.

Ann Loraine added a comment - 28/May/24 1:40 PM - edited Do the above, but for SL4: gunzip -c S_lycopersicum_Sep_2019.bed.gz | grep Solyc02g083860 > txt.bed Edit txt.bed; replace final field with text: anthocyanin-reduced (are) flavanone 3-hydroxylase (F3H) Replace old line with new one and make tabix index: gunzip -c S_lycopersicum_Sep_2019.bed.gz | grep -v Solyc02g083860 > S_lycopersicum_Sep_2019.bed cat txt.bed S_lycopersicum_Sep_2019.bed | sort -k1,1 -k2,2n | bgzip > S_lycopersicum_Sep_2019.bed.gz Make index, with special options: local aloraine$ tabix -s 1 -b 2 -e 3 S_lycopersicum_Sep_2019.bed.gz [W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option? local aloraine$ tabix -s 1 -b 2 -e 3 -0 S_lycopersicum_Sep_2019.bed.gz [tabix] the index file exists. Please use '-f' to overwrite. local aloraine$ tabix -s 1 -b 2 -e 3 -0 -f S_lycopersicum_Sep_2019.bed.gz

Ann Loraine added a comment - 28/May/24 1:52 PM New files are now available in subversion repository version 191 and above.

Ann Loraine added a comment - 28/May/24 1:53 PM Review the gene descriptions for the gene in SL4 and SL5. If it's OK, move to Done.

Paige Kulzer added a comment - 30/May/24 9:59 AM The spelling error has been corrected. I was able to search for this gene and find it easily in both SL4 and SL5. Moving to Done.