Potentially useful code is available here:

• https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/
• https://bitbucket.org/hotpollen/rna-seq/src/master/

Check out the code used to read the BED annotation files.

In the "bed-detail" file from IGB Quickload:

• Each row represents a transcript (also called a "gene model")
• Field 3 is a transcript identifier, one per row
• Field 13 is the gene identifier.

Need Reviewing:

I commit new code to bitbucket for file 'MappingNames.Rmd'.

https://bitbucket.org/mdavis4290/splicing-analysis/src/master/DescriptionMapping/MappingNames.Rmd

[~aloraine]

Currently working on code for checking merge.
Still learning git commands!

[~molly] - please submit PR from your fork's master branch to the team repository master branch. Use the Bitbucket interface; google "how to submit PR using bitbucket" for tips if required.

Made a pull request for the master branch for file 'MappingNames.Rmd'.

Notes include:

• Added correct files with all of the data included.
• Made write commands to save files to local machine.
• Creates two files. The first one includes the exact columns Ann requested. The second one looks like the original bed file SL5 but now with the descriptions.

[~aloraine]

Testing "MappingNames.Rmd" in https://bitbucket.org/hotpollen/splicing-analysis/src/master/DescriptionMapping/.

An issue:

• Markdown fails to compile (knit) due to files not being present on my system. Paths are hard-coded to a location not on my computer:

SL5.fname="/Users/mollydavis333/Desktop/S_lycopersicum_Jun_2022.bed"
SL4.fname="/Users/mollydavis333/Desktop/S_lycopersicum_Sep_2019.bed"
...
mapping.fname="/Users/mollydavis333/Desktop/SL4-SL5_covert.tsv"

This can be fixed by directly accessing the files using relative paths as these are version controlled in splicing_analysis/ExternalData.
R can open "gzip'd" files. No need to uncompress them first. Google "read compressed data file into R" or something to see how this can be done.

attn: [~molly]

Link to updated mapping file on bitbucket under Molly fork:

https://bitbucket.org/mdavis4290/splicing-analysis/src/master/DescriptionMapping/MappingNames.Rmd

Not sure why there is a conflict. I have committed changes and when I try to 'git merge remotes/origin/master' it says that it is already up to date.

Will need help making pull request with conflict in the way.

[~aloraine]

PR is merged and code is ready for review and testing.

The .Rmd file can't "knit".
I think this is due to the final line of one of the code chunks in which a large data frame is being printed to the document.
So I ran the file interactively, chunk by chunk.
This resulted in creating two data files, one with identifiers and another that tries to be a BED file.
However, when I opened the BED file in IGB, I got an error:

09:03:26.741 ERROR c.a.igb.view.load.GeneralLoadUtils - Error in loadOnSequence
java.lang.NumberFormatException: For input string: ""270"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) ~[na:1.8.0_332]
at java.lang.Integer.parseInt(Integer.java:569) ~[na:1.8.0_332]
at java.lang.Integer.parseInt(Integer.java:615) ~[na:1.8.0_332]
at com.affymetrix.genometry.parsers.BedParser.parseIntArray(BedParser.java:414) ~[genometry-9.1.10.jar:na]
at org.lorainelab.igb.bed.BedSymloader.parseLine(BedSymloader.java:310) ~[na:na]
at org.lorainelab.igb.bed.BedSymloader.parseLines(BedSymloader.java:184) ~[na:na]
at org.lorainelab.igb.bed.BedSymloader.parse(BedSymloader.java:170) ~[na:na]
at org.lorainelab.igb.bed.BedSymloader.parse(BedSymloader.java:146) ~[na:na]
at org.lorainelab.igb.bed.BedSymloader.getRegion(BedSymloader.java:139) ~[na:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:287) ~[genometry-9.1.10.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:164) ~[genometry-9.1.10.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139) ~[genometry-9.1.10.jar:na]
at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119) ~[genometry-9.1.10.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:749) ~[igb-9.1.10.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.loadOnSequence(GeneralLoadUtils.java:664) [igb-9.1.10.jar:na]
at com.affymetrix.igb.view.load.GeneralLoadUtils$1.lambda$multiThreadedLoad$178(GeneralLoadUtils.java:607) [igb-9.1.10.jar:na]
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) ~[na:1.8.0_332]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_332]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) ~[na:1.8.0_332]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ~[na:1.8.0_332]
at java.lang.Thread.run(Thread.java:750) ~[na:1.8.0_332]

I looked at the BED file in Terminal and observed that many of the fields have quotation marks around them.
This is likely the cause of the error, as IGB reports failing due to a NumberFormatException when attempting to
parse "270

The table output command needs to indicate that no quotation marks will be used.
Moving back to "To-Do"

Next steps:

• Modify the output file format to not wrap any of the fields with quotation marks.
• Modify the code chunk to no longer print out an entire data frame to the final knitted document
• Ensure that the file can "knit" without error

Moving the above request changes into a new ticket and closing this one.

Update:

• Aligned SL4 gene models onto SL5 genome assembly using blat.sh:

#!/bin/bash
G=S_lycopersicum_Jun_2022
D=$G.2bit
Q=S_lycopersicum_Sep_2019_models_cDNA.fa
PSL=SL42SL5.psl
MI=15000
blat -noTrimA -maxIntron=$MI -noHead -minIdentity=95 -dots=100 $D $Q $PSL

• Sorted and tabix-indexed PSL output file with:

sort -k14,14 -k16,16n SL42SL5.psl | bgzip -c > SL42SL5.psl.gz
tabix -s 14 -b 16 -e 17 SL42SL5.psl.gz

• Added output and code to repository - bitbucket.org/hotpollen/splicing-analysis.git

Reference: https://bitbucket.org/lorainelab/affyprobesetsforigb/src/master/ (documents how to make a tabix-indexed file from PSL blat output)

Update:

Modifying SL5 description field to include SL4 locus identifier, for example:

hexokinase-1 protein (AHRD V3.3 *** AT1G05205.1)

becomes:

hexokinase-1 protein (AHRD V3.3 *** AT1G05205.1) ITAG4.0:Solyc07g052420.3

Added new file to svn repository after creating tabix-indexed file with:

sort -k1,1 -k2,2n ~/src/splicing-analysis2/DescriptionMapping/output/S_lycopersicum_Jun_2022.bed | bgzip > S_lycopersicum_Jun_2022.bed.gz 
tabix -s 1 -b 2 -e 3 S_lycopersicum_Jun_2022.bed.gz

svn repo info:

• Browse by visiting https://svn.bioviz.org/viewvc/
• svn repo URLs:

  URL: https://svn.bioviz.org/repos/genomes/quickload/S_lycopersicum_Jun_2022
  Repository Root: https://svn.bioviz.org/repos/genomes

• to check out the repo using read-only user, enter user name "guest" password "guest"

Updated quickload sites on RENCI and UNCC hosting.

At UNCC, logged in with:

ssh -J aloraine@cci-jump.uncc.edu -p 1657 aloraine@igbquickload.org

At RENCI, logged in with:

ssh -J aloraine@hop.renci.org aloraine@lorainelab-quickload.scidas.org