Example file

[dorimolnar]

Der Output, den der Typ für das Example File bekommt, ist nicht korrekt. Sowohl die Best Matches (TFs mit ähnlicher Bindungsspezifität) als auch die vorhergesagte PFM ist falsch. Eigentlich sollte das hier rauskommen:
https://github.com/draeger-lab/SABINE/blob/edba8d5198ac8f3eb84ea35942f310fa6fff3c81/doc/example.output.txt

Offensichtlich gibt es ein Problem mit der PSIPRED-Dependency von SABINE. Ich nehme an das Tool wurde nicht richtig installiert. In der SABINE-Doku steht dazu folgendes:

Moeglicherweise hat er die tcsh shell nicht installiert. Das ist eine Dependency von PSIPRED, die meist nicht standardmaessig auf Unix-Systemen installiert ist. Bei PSIPRED sind übrigens auch Demo-Daten dabei, mit denen man die Installation testen kann. Das ist hier beschrieben:
https://github.com/draeger-lab/SABINE/blob/edba8d5198ac8f3eb84ea35942f310fa6fff3c81/lib/PSIPRED/readme
Wahrscheinlich reicht es aber aus das Unix-Paket für die tcsh shell zu installieren und dann das install.sh Skript nochmal laufen zu lassen.

English
The output that the type receives for the example file is not correct. Both the best matches (TFs with similar binding specificity) and the predicted PFM are incorrect. This is what should actually come out here:
https://github.com/draeger-lab/SABINE/blob/edba8d5198ac8f3eb84ea35942f310fa6fff3c81/doc/example.output.txt

Obviously there is a problem with the PSIPRED dependency of SABINE. I assume the tool was not installed correctly. The SABINE documentation says the following:

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I've tried re-installing SABINE and manually creating a /tmp directory prior to its execution. It looks like it worked, but there's a warning/error that appear every time SABINE is run: "./lib/PSIPRED/lylzzvhrac.horiz (No such file or directory)" where "*.horiz" changes each run. This also appears when ./sabine.sh -check-install is run.

For reference, this is how I test ran SABINE with the example input file (the one the comes with the git package):
$ ./sabine.sh example.input.txt

Meanwhile the output file (example.input.txt.out) looks like this:

NA T01963
XX
BM T00193 0.6595704528587462
BM T04840 0.6595704528587462
BM T04665 0.6595704528587462
BM T04256 0.6595704528587462
BM T04255 0.6595704528587462
XX
MA 0 50 7 8 35 w
MA 1 72 4 8 16 A
MA 2 3 3 5 89 T
MA 3 41 2 0 57 W
MA 4 85 3 0 12 A
MA 5 43 1 51 5 R
MA 6 1 6 2 91 T
MA 7 41 23 10 26 N
MA 8 32 18 4 46 n
MA 9 51 2 16 31 w
XX
//
XX

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I played around with it a bit and found that SABINE attempted to create multiple folders at once but called the wrong method for doing so. After manually creating an empty directory tmp directly in the SABINE base folder that error went away.

I also uploaded the missing example files and fixed problems with outdated links in the README file today.

Please see my comments on GitHub on the matter as well.

Unfortunately, I can't do much more at the moment because SABINE only runs on Linux but I am on a Mac now. The executables don't work in my installation. If you continue to run into trouble, we can check what can be done.

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I was wondering if you had the chance to look into the error Warning/Error that was encountered during installation of SABINE and whether this warning can be safely ignored.

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The test output is the one generated by TFpredict (specifying -sabineOutfile).