error in expMatrixToBarchartBed

[Hideya Kawaji]

Dear UCSC genome browser team,

I found an issue of expMatrixToBarchartBed, in particular working in
Ubuntu 22.04,
when following the instruction at
https://genome.ucsc.edu/goldenPath/help/barChart.html

It seems to be caused by a difference of system shell (note that dash
is being used in Ubuntu, instead of bash), and I could manage it by
modification
of a single line.

--------

### working at ubuntu
$ cat /etc/os-release | grep PRETTY_NAME
PRETTY_NAME="Ubuntu 22.04.3 LTS"

### prepare files
$ printf "chr14\t95086227\t95158010\tENSG00000100697.10\t999\t-\tDICER1\n"
> example.bed
$ wget https://genome.ucsc.edu/goldenPath/help/examples/barChart/exampleSampleData.txt
$ wget https://genome.ucsc.edu/goldenPath/help/examples/barChart/exampleMatrix.tx
$ wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/expMatrixToBarchartBed
$ chmod +x expMatrixToBarchartBed

### run the original script. It caused an error with no output in stdout.
$ ./expMatrixToBarchartBed exampleSampleData.txt exampleMatrix.txt
example.bed /dev/stdout
#chr chromStart chromEnd name score strand name2
expCount expScores;adiposeSubcut breastMamTissue
colonTransverse muscleSkeletal wholeBlood _offset _lineLength
Couldn't open /tmp/tmpXRyn8n , No such file or directory

### run a modified script (see the difference below). It successfully
produced the output
$ ./expMatrixToBarchartBed_edit exampleSampleData.txt
exampleMatrix.txt example.bed /dev/stdout
#chr chromStart chromEnd name score strand name2
expCount expScores;adiposeSubcut breastMamTissue
colonTransverse muscleSkeletal wholeBlood _offset _lineLength
chr14 95086227 95158010 ENSG00000100697.10 999
- DICER1 5 11,12,8,6.7,4.9 93153 26788

### the difference of the scripts
$ $ diff expMatrixToBarchartBed expMatrixToBarchartBed_edit
329c329,330
< if not options.verbose: cmd += " &>/dev/null"
---
> #if not options.verbose: cmd += " &>/dev/null"
> if not options.verbose: cmd += " 2>&1 >/dev/null"

----

best,
Hideya

--
KAWAJI, Hideya, Ph.D <kawa...@igakuken.or.jp>
Associate Center Director, Research Center for Genome & Medical Sciences,
Tokyo Metropolitan Institute of Medical Science (TMiMS)
tel: 03-5316-3128 (ex. 3140) http://www.igakuken.or.jp/genome-center/

[Matthew Speir]

Hello, Hideya.

Thank you for reporting this issue with expMatrixToBarchartBed. We've now patched the tool.

We were also curious about how you're using the bar chart tracks in your work?

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---

Matthew Speir

UCSC Genome Browser, User Support

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[Hideya Kawaji]

Dear Matthew,

Great to hear that it's been fixed. Fully appreciated.

barChart is very useful for us to visualize promoter/enhancer (in
BED6) activities across the samples on the genomic view.
It would be more beneficial if gene structure (in BED12) could be
displayed in an isoform distinguishable manner, alongside the
expression chart.

best,
Hideya

--
KAWAJI, Hideya, Ph.D <kawa...@igakuken.or.jp>
Associate Center Director, Research Center for Genome & Medical Sciences,
Tokyo Metropolitan Institute of Medical Science (TMiMS)
tel: 03-5316-3128 (ex. 3140) http://www.igakuken.or.jp/genome-center/

2024年7月20日(土) 8:46 Matthew Speir <msp...@ucsc.edu>: