reading CLAN output (.cex files) into R

[Leonid Spektor]

Rose,

	All CLAN input and output files are in plain text format and can be opened by any text editor. The problem you seems to be encountering is due to R application's failure to recognize files with .cex as text files. You can change CLAN's output filename extension either by locating that file on the hard disk and renaming it from .cex to .txt manually or you can use CLAN's rename command "ren" to do it. Here is the rename command "ren *.cex *.txt".

	The reason the +f.txt option works the way it does is because files are associated with applications based in their filename extensions. And we wanted to allow people to change some part of the filename extension without losing those files association with CLAN application. The reason for that is that even though CLAN output files are encoded in plain text format some text editor might still be unable to display some CLAN files correctly. In particular any file that has underlines or has any non-english characters would have to be opened in a special way by other text editor. CLAN files are encoded in UTF-8. If text editor or your program R is unable to display CLAN files correctly automatically, then you will have to instruct that application to treat CLAN output files as "plain text", UTF-8 encoded files.

Leonid.



On Jun 5, 2013, at 02:42 , rose maier wrote:

> Hello,
> I am running CHIP on several transcripts, and I would like to import the output statistics into another program (R) for analysis. In particular, I want to be able to read in the ADU, CHI, ASR, and CSR stats (the +d1 portion of the output). R doesn't seem able to read the .cex files (I am using the R function read.table, if you happen to be familiar with that), so I was hoping to switch the CLAN output format to something like .txt instead. In the manual, the section on the +f switch seems to suggest that it is possible to change the file extension by typing +f.txt, but when I do this, I just get files that end with ".txt.cex". I've tried it with and without quotes around the .txt in the +f switch, and with several commands other than CHIP, such as FREQ and KWAL. I continue to get .txt.cex files in my output folder no matter what I do. 
> This is the command I'm using in CLAN:
> chip +bMOT +cCHI +g +harticles.cut +hsubpro.cut +hpronounobjs.cut -hexclude.cut +d1 +f.txt *.cha
> I'm running it on a MacBook Pro (OSX 10.6.8) and I'm pretty sure I'm using the most recent version of CLAN (I re-installed it about a week ago). 
> Any assistance you can provide would be much appreciated. Or perhaps there is a totally different, more straight forward way to export CLAN output into data tables or spreadsheets? 
> Thanks in advance,
> Rose Maier
> 
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