search

kroganlab / mist

mist R package files
GNU General Public License v3.0
9 stars 2 forks source link

[BUG] Remove and collapse files are not actually optional #16

Open marcus-r-kelly opened 9 years ago

marcus-r-kelly commented 9 years ago

MiST is exiting with an error if : 1) no remove line is supplied in the config YAML 2) a remove line is supplied in the config YAML with a blank argument 3) a remove line is supplied in the config YAML whose argument is an existing, but empty file.

The above is also true for the "collapse" file. I am using, as far as I can tell, the latest MiST version.

jvondollen commented 9 years ago

Thanks for the feedback. Currently, Mist is set up so that the only files that are required to have information in them are the "data" and "keys" files. The other files (collapse, remove, specificity_exclusions) must exist, but you can leave them as empty text files if you plan to not apply their constraining ability to the scoring algorithm. We'll look into making the actual files more optional.

marcus-r-kelly commented 9 years ago

Actually, MiST isn't running even with empty files for remove and collapse. In order to get it to work without removing samples, I had to supply a remove file with the content "foo bar" ; in the collapse file, I used "bait1 bait1"

jvondollen commented 9 years ago

The YAML file needs to be structured as the sample file, with no lines removed. If this isn't the problem, perhaps you could share the error output and the YAML file?

On Mon, Sep 14, 2015 at 11:11 AM, mrkusrk notifications@github.com wrote:

Actually, MiST isn't running even with empty files for remove and collapse. In order to get it to work without removing samples, I had to supply a remove file with the content "foo bar" ; in the collapse file, I used "bait1 bait1"

— Reply to this email directly or view it on GitHub https://github.com/kroganlab/mist/issues/16#issuecomment-140163601.

jvondollen commented 9 years ago

Were you able to get the test set called "small" to run? All of the files listed in the YAML file are sourced from the root directory?

marcus-r-kelly commented 9 years ago

Yes, and yes.

On Tue, Sep 15, 2015 at 10:56 AM jvondollen notifications@github.com wrote:

Were you able to get the test set called "small" to run? All of the files listed in the YAML file are sourced from the root directory?

— Reply to this email directly or view it on GitHub https://github.com/kroganlab/mist/issues/16#issuecomment-140482131.

jvondollen commented 9 years ago

I do not have this issue and I have not been able to reproduce your problem. What is the exact error output. I need more information to narrow down your issue since this has not been a problem for any other machine. I have added a patch that handles the case where the file is missing, but that shouldn't have any impact on the case when the file is empty.

marcus-r-kelly commented 9 years ago

Well, now I can't get it to reproduce. Huh.

Well, thanks for your effort, and feel free to close this.