michaelkyu/ddot

Toolkit for constructing, analyzing, and visualizing data-driven ontologies

ddot's Issues

Tulip does not work on python37

Right now, there hasn't been a wheel added for py37 so it can't yet be used. It seems like they do not have their source code publicly available so I don't think it's an option to build from scratch either...

EmptyDataError when running Clixo

I am trying to run CliXO on a pairwise matrix of gene similarity scores. If I'm understanding the error message correctly, the temporary table generated to store the ontology is empty and resulting in this error. Do you know why that is? Or, if I am reading the error message incorrectly, could you elaborate on how I can go about fixing the issue?

CliXO_HPAbicor.pdf
HPA_bicor.csv

unable to pull any of the two docker images

I am trying to use ddot by using docker. As in subject line, I am unable to pull any of the two docker images:

kratz@kratz-VirtualBox:~ (master) $ docker pull michaelkyu/ddot-anaconda2
Using default tag: latest
Error response from daemon: manifest for michaelkyu/ddot-anaconda2:latest not found
kratz@kratz-VirtualBox:~ (master) $ docker pull michaelkyu/ddot-anaconda3
Using default tag: latest
Error response from daemon: manifest for michaelkyu/ddot-anaconda3:latest not found

Ddot Tutorial Error

Hi, I installed all of the packages required to run ddot per instructions and cloned the repository, and I was trying to run the tutorial notebook in Jupyter. When I try to construct the ontology in the tutorial, I get this error:

TypeError Traceback (most recent call last)
in
20
21 # Construct ontology
---> 22 ont = Ontology(hierarchy, mapping)
23
24 # Prints a summary of the ontology's structure

~\Anaconda3\lib\site-packages\ddot\Ontology.py in init(self, hierarchy, mapping, edge_attr, node_attr, parent_child, add_root_name, propagate, ignore_orphan_terms, verbose, **kwargs)
606
607 if edge_attr is None:
--> 608 self.clear_edge_attr()
609 else:
610 assert edge_attr.index.nlevels == 2

~\Anaconda3\lib\site-packages\ddot\Ontology.py in clear_edge_attr(self)
709
710 self.edge_attr = pd.DataFrame()
--> 711 self.edge_attr.index = pd.MultiIndex(levels=[[],[]],
712 labels=[[],[]],
713 names=['Child', 'Parent'])

TypeError: new() got an unexpected keyword argument 'labels'

It seems to be an error in the source code.

CalculateFDR failed to write the FDRs output

I got this error sed: -e expression #1, char 5: unknown command: `'after all the iterations are done, and then the FDRs output is blank. I figured that there may be something wrong with writing the final outputs. Then I found that the error is from the line 47-51 in the CalculateFDR function:
for i in $(seq 0 $(($NUM_ITER - 1)) )
do
END_OF_HEADER=$(grep -n Matched $RESULTS_DIR/rand_files/alignment_"$i" | sed 's/:.*//');
sed "1,$END_OF_HEADER""d" $RESULTS_DIR/rand_files/alignment_"$i" | sort -r -n -k 3 | cut -f 1,2,3 > $RESULTS_DIR/rand_files/alignment_without_descendents_$i
done

This loop looks for the line number where 'Matched' occurs in the file and gathers information after that line. However, for some of my alignment files, there are 2 'Matched' in the file, which leads to an error when generating "alignment_without_descendents" file. I am curious what causes the additional 'Matched' to appear in the file? Thanks

Pre-compiled CLIXO does not work

Having pre-compiled C++ code in the repository is a bit confusing, since it doesn't generally work on each person's system. This isn't obvious from using the python code, since using subprocess.Popen fails completely silently if the current system can't run the clixo binary. Note: I'm running Mac OS 11.13 Sierra with the following clang:

$ g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.11.45.2)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Further, I went to re-compile myself and got the following error due to the inclusion of the -static flag to include static libraries:

$ make clean
rm *.o
(ddot) [529] [13:20] [cthoyt@wlan-224:~/dev/ddot/ddot/mhk7-clixo_0.3-cec3674]
$ make all
g++ -Wall -O4 -c -std=c++11 -fomit-frame-pointer -funroll-loops -fforce-addr -fexpensive-optimizations -static -I . clixo.cpp
clang: warning: -O4 is equivalent to -O3 [-Wdeprecated]
clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument]
In file included from clixo.cpp:3:
./dagConstruct.h:850:32: warning: '/*' within block comment [-Wcomment]
    /*if ((printClusterInfo && /*!combiningNow &&*//* !currentClusters[clusterToDelete].wasCheckedFinal()) || (currentClusters[clusterToDelete]...
                               ^
./dagConstruct.h:932:14: warning: '/*' within block comment [-Wcomment]
      /*if ((/*!combiningNow && *//*!clusterToExtend_it->wasCheckedFinal()) || clusterToExtend_it->isValid()) {
             ^
./dagConstruct.h:1403:17: warning: private field 'numClusters' is not used [-Wunused-private-field]
  unsigned long numClusters;
                ^
3 warnings generated.
g++ -Wall -O4 -std=c++11 -fomit-frame-pointer -funroll-loops -fforce-addr -fexpensive-optimizations -static -I . clixo.o -o clixo
ld: library not found for -lcrt0.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [clixo] Error 1

I'm not much of a dev-ops person and I'm still working through the issue, but this thread had some information that sort of worked: https://discussions.apple.com/thread/1945589?answerId=9213715022#9213715022. It suggested removing the -static flags, or even better, adding more conditionals in the makefile to check what system is being run and if this is a good idea or not. After, I was able to re-compile it and got the following output:

$ make clean
rm *.o
(ddot) [533] [13:23] [cthoyt@wlan-224:~/dev/ddot/ddot/mhk7-clixo_0.3-cec3674]
$ make all
g++ -Wall -O4 -c -std=c++11 -fomit-frame-pointer -funroll-loops -fforce-addr -fexpensive-optimizations -I . clixo.cpp
clang: warning: -O4 is equivalent to -O3 [-Wdeprecated]
clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument]
In file included from clixo.cpp:3:
./dagConstruct.h:850:32: warning: '/*' within block comment [-Wcomment]
    /*if ((printClusterInfo && /*!combiningNow &&*//* !currentClusters[clusterToDelete].wasCheckedFinal()) || (currentClusters[clusterToDelete]...
                               ^
./dagConstruct.h:932:14: warning: '/*' within block comment [-Wcomment]
      /*if ((/*!combiningNow && *//*!clusterToExtend_it->wasCheckedFinal()) || clusterToExtend_it->isValid()) {
             ^
./dagConstruct.h:1403:17: warning: private field 'numClusters' is not used [-Wunused-private-field]
  unsigned long numClusters;
                ^
3 warnings generated.
g++ -Wall -O4 -std=c++11 -fomit-frame-pointer -funroll-loops -fforce-addr -fexpensive-optimizations  -I . clixo.o -o clixo
g++ -Wall -O4 -c -std=c++11 -fomit-frame-pointer -funroll-loops -fforce-addr -fexpensive-optimizations -I . clustersToDAG.cpp
clang: warning: -O4 is equivalent to -O3 [-Wdeprecated]
clang: warning: optimization flag '-fexpensive-optimizations' is not supported [-Wignored-optimization-argument]
In file included from clustersToDAG.cpp:3:
./dagConstruct.h:850:32: warning: '/*' within block comment [-Wcomment]
    /*if ((printClusterInfo && /*!combiningNow &&*//* !currentClusters[clusterToDelete].wasCheckedFinal()) || (currentClusters[clusterToDelete]...
                               ^
./dagConstruct.h:932:14: warning: '/*' within block comment [-Wcomment]
      /*if ((/*!combiningNow && *//*!clusterToExtend_it->wasCheckedFinal()) || clusterToExtend_it->isValid()) {
             ^
./dagConstruct.h:1403:17: warning: private field 'numClusters' is not used [-Wunused-private-field]
  unsigned long numClusters;
                ^
3 warnings generated.
g++ -Wall -O4 -std=c++11 -fomit-frame-pointer -funroll-loops -fforce-addr -fexpensive-optimizations  -I . clustersToDAG.o -o clustersToDAG

[`to_ndex`] "description" field does not actually upload from ddot into NDEx

With the to_ndex function, it seems that the "description" field does not actually upload from ddot into NDEx. Or it uploads but NDEx does not accept it. The description field could be extremely useful (I am uploading a large number of hierarchies and am auto-generating description text which describes model building parameters, data provenance etc), but it does not seem to get into NDEx, the "description" field there is just empty.

url, _ = ont.to_ndex(name="sho6Nooz",
  description="a_0.07_b_0.5_m_0.004_z_0.1, cutoff 0.287 algnmt GO BP DNA Repair",
  ndex_server='http://test.ndexbio.org',
  ndex_user='kratz',
  ndex_pass='XXXXXXXX',
  network=sim_long,
  main_feature='similarity',
  layout='bubble-collect')

I have described this issue in the Cytoscape Slack on 2019-01-19.

Servers I'm using: http://test.ndexbio.org, http://hiview-test.ucsd.edu, http://hiview.ucsd.edu​