Dot to XDSL Module Progress

Module that implements conversion of dot format to Genie Bayesian Network format

Dot to XDSL Module Progress

Postby vlee14 » Thu Dec 11, 2014 3:07 pm

The Dot to XDSL Module converting the dot file to an xdsl file and adding paramaters from the dataset using the SMILE EM module, has been tested and completed today.
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Re: Dot to XDSL Module Progress

Postby meninonas » Wed Jan 14, 2015 12:43 pm

Dr. Yoo,

I have tested the module with the DREAM2 Challenge 3 FjveGene_qPCR dataset and it worked properly.

Please find the corresponding files and results attached.
Attachments
output.xdsl
(2.14 KiB) Downloaded 133 times
InputFile.dot
(297 Bytes) Downloaded 145 times
Dataset.txt
(275 Bytes) Downloaded 123 times
Last edited by meninonas on Tue Jan 20, 2015 11:39 am, edited 1 time in total.
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Posts: 137
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Re: Dot to XDSL Module Progress

Postby meninonas » Wed Jan 14, 2015 1:54 pm

Dr. Yoo,

I just ran Hamza's dataset and I ran into the following error:

Code: Select all
terminate called after throwing an instance of 'bnl::io_error'
  what(): I/O Error:Unable to add node to network.
Aborted (core dumped)


I've changed the names and it did not improve. In addition, I went over the inputs (InputFile.dot and Dataset.txt) and they matched up so I'm uncertain why the code is not working.

I highlighted the error to Vincent and he said he would look into it.
Attachments
InputFile.dot
(5.91 KiB) Downloaded 135 times
Dataset.txt
(48.15 KiB) Downloaded 139 times
meninonas
 
Posts: 137
Joined: Tue Jun 24, 2014 3:25 pm

Re: Dot to XDSL Module Progress

Postby meninonas » Thu Jan 15, 2015 2:51 pm

Dr. Yoo,

The dot-to-xdsl module was tested with the DREAM2 Challenge 3 FiveGene_chip-3 dataset and it was successful.

Please see the corresponding files and results below.
Attachments
output.xdsl
(9.75 KiB) Downloaded 134 times
InputFile.dot
(1.13 KiB) Downloaded 122 times
Dataset.txt
(951 Bytes) Downloaded 152 times
Last edited by meninonas on Tue Jan 20, 2015 11:39 am, edited 1 time in total.
meninonas
 
Posts: 137
Joined: Tue Jun 24, 2014 3:25 pm

Re: Dot to XDSL Module Progress

Postby meninonas » Fri Jan 16, 2015 3:46 pm

Dr. Yoo,

The dot-to-xdsl module was tested on the DREAM2 Challenge 4 InSilico1-heterozygous-2 dataset and it was successful.

Please see the corresponding files and results below.
Attachments
output.xdsl
(22.43 KiB) Downloaded 134 times
InputFile.dot
(2.34 KiB) Downloaded 118 times
Dataset.txt
(5.17 KiB) Downloaded 130 times
meninonas
 
Posts: 137
Joined: Tue Jun 24, 2014 3:25 pm

Re: Dot to XDSL Module Progress

Postby meninonas » Tue Jan 20, 2015 1:52 pm

Dr. Yoo,

The dot-to-xdsl module was tested on the DREAM2 Challenge 4 InSilico1-null-mutants dataset and it was not successful. It gave me the following error.

Code: Select all
Cannot read the data file... existing.


This code was given to me even after I formatted the dataset in two different instances.

Something that I've noticed is that the code seems to be highly specific with the way it is formatted, i.e., the code does not accept tab or comma separated columns, just space separated files.

Please see the files below.
Attachments
InputFile.dot
(2.43 KiB) Downloaded 136 times
Dataset.txt
(5.17 KiB) Downloaded 127 times
meninonas
 
Posts: 137
Joined: Tue Jun 24, 2014 3:25 pm


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