generateReport failing to open pdf

roblanf / sangeranalyseR

functions to analyse sanger sequencing reads in R

MIT License

95 stars 24 forks source link

generateReport failing to open pdf #57

Closed camilogarciabotero closed 3 years ago

camilogarciabotero commented 3 years ago

Hi @Kuanhao-Chao ,

Thanks for working on this project! This is could be the best open-source alternative to analyze sanger sequences I've ever found on the web!

I could spot this problem when generating the report of my SA. That is, when running generateReport() function on my SA got the following error:

Error in pdf(filename, width = 8.5, height = height * numplots) : cannot open file './SangerAlignment/302_M1_groEL/302_M1_groEL_1_F/Chromatogram.pdf'

It seems that maybe there is no .PDF or it is not being exported correctly. Anyway, It would be great if you have any thoughts to solve it!

Cheers, Camilo.

Kuanhao-Chao commented 3 years ago

Hi @camilogarciabotero,

Sorry for my late reply. I just checked the generateReport() function, and it seems that it works fine. If there's any chance you can send me your ab1 files to kuanhao.chao@gmail.com, that would really help. Of course, I'll only use them for fixing this bug!

Cheers,

Kuan-Hao

camilogarciabotero commented 3 years ago

Hi @Kuanhao-Chao

Thanks for your answer. When trying this function as suggested:

generateReport(newSangerRead,
               outputDir = tempdir()
)

Worked for me, yet the HTML report is quite different from what the direct report of the function launchApp()renders. Is this what the report should look like when using the function?

Also, when using it with another outpuDir path, the execution was halted as I mentioned above. I'll try to send the sequences soon.

Thank you, Camilo.

Kuanhao-Chao commented 3 years ago

Hi @camilogarciabotero,

I tested the generateReport function again and found that the function will crash if you give relative path instead of the absolute path. I have fixed this bug in the newest commit. Please rerun your function again and let me know whether it works.

And for the HTML report, the layout of it is different from Shiny apps, but the results stored inside are same as the results in Shiny apps.

Cheers,

Kuan-Hao

camilogarciabotero commented 3 years ago

Hey Kuan-Hao,

Thanks for your support. I got this other message when using a relative path with the last commit version:

Quitting from lines 303-318 (SangerRead_Report_ab1.Rmd) 
Error in pdf(filename, width = 8.5, height = height * numplots) : 
  cannot open file './/SangerAlignment/302_M1_groEL/302_M1_groEL_1_F/Chromatogram.pdf'

Regards, Camilo.

Kuanhao-Chao commented 3 years ago

Hi @camilogarciabotero

I fixed the relative path problems in both writeFasta and generateReport functions and updated it in the latest commit. Both generateReport(sangerAlignment, "./output_directory") and writeFasta(sangerAlignment, "./output_directory") should work correctly now.

Sorry for my late reply.

cheers, Howard