biopp / bppsuite Goto Github PK

View Code? Open in Web Editor NEW

14.0 14.0 12.0 1.41 MB

Bio++ Program Suite

CMake 3.38% C++ 96.15% Shell 0.46%

bppsuite's People

Stargazers

Watchers

Forkers

matsen matsengrp transgirlcodes altingia caesantibanez halabikeren shuifeng1988 anatshafir1 luisdiaz1997 psathyrella standardgalactic mr-c

bppsuite's Issues

bppseqgen GTR model parameters

Hi,
Could you share what the parameters mean (a, b, c, d, e, theta, theta1, theta2) in bppgenseq of GTR model, I didn't find any explanation about these parameters, could you share your help? thank you very much.

In bppseqgen parameter file setting:
#model
model=GTR(a,b,c,d,e,theta,theta1,theta2)

CodonSiteStatistics - output.file

Hi,

I could not specify an output.file via the cmd arguments and it seems that an argument within the option params could not be set.

In bash it seems to be not supported to create a variable with a . inside the name:

see bash export man

   name   A  word  consisting  only  of alphanumeric characters and under‐
          scores, and beginning with an alphabetic character or an  under‐
          score.  Also referred to as an identifier.

As a work-around I now changed the following lines of and re-compiled:

https://github.com/BioPP/bppsuite/blob/master/bppSuite/bppPopStats.cpp

      // +-----------------------+
      // | Codon site statistics |
      // +-----------------------+
      else if (cmdName == "CodonSiteStatistics")
      {
        if (!codonAlphabet) {
          throw Exception("CodonSiteStatstics can only be used with a codon alignment. Check the input alphabet!");
        }
        string path = ApplicationTools::getAFilePath("output.file", cmdArgs, true, false);

into

      // +-----------------------+
      // | Codon site statistics |
      // +-----------------------+
      else if (cmdName == "CodonSiteStatistics")
      {
        if (!codonAlphabet) {
          throw Exception("CodonSiteStatstics can only be used with a codon alignment. Check the input alphabet!");
        }
        string path = ApplicationTools::getAFilePath("output.file", bpppopstats.getParams(), true, false);

Now, an output.file argument can be set in the option params file.

Maybe think of a better explanation in the manual, how to set with command arguments.

WARNING!!! Parameter output.file not specified. Default used instead: none
You must specify a file for this parameter: output.file

Thank you in anticipation

Best regards

Kristian Ullrich

bppseqgen expected to ignore branch length from root to mrca?

It appears that bppseqgen doesn't mutate according to the distance between root and mrca. For instance using a tree like:

(t1:0.001,t2:0.001):0.1;

results in two essentially unmutated sequences. Adding a dummy leaf xxx branched from root to this tree, on the other hand, results in the expected mutation rates:

((t1:0.001,t2:0.001):0.1,xxx:0.101):0.0;

This seems like unexpected behavior to me, but perhaps I'm missing something?

bppsuite 3.0.0 relies on not yet published bpp-phyl

Hi,
I tried to update the bppsuite package in Debian. When I try to build bppsuite 3.0.0 but it is seeking header files in different places than in libbpp-phyl 2.4.1 which is packaged for Debian. For instance the header files that reside in Bpp/Phyl/Tree.h are seeked in Bpp/Phyl/Tree/Tree.h. I suspect you are using a higher version of the library but this is not yet tagged on Github.
Kind regards, Andreas.

compilation error - v3

Hi,

I could not compile v3.0.0 due to the following dependency Eigen3 and after installing Eigen3 some more compiling warnings popped up.

-- Found /usr/bin/gzip compression program, using file extension .gz
-- bpp-core 4.1.0 found:
--   static lib: /opt/biosoftware/bppsuite/build/lib/libbpp-core.a
--   shared lib: /opt/biosoftware/bppsuite/build/lib/libbpp-core.so.4.1.0
--   includes: /opt/biosoftware/bppsuite/build/include
-- bpp-seq 12.0.0 found:
--   static lib: /opt/biosoftware/bppsuite/build/lib/libbpp-seq.a
--   shared lib: /opt/biosoftware/bppsuite/build/lib/libbpp-seq.so.12.0.0
--   includes: /opt/biosoftware/bppsuite/build/include
-- bpp-phyl 12.0.0 found:
--   static lib: /opt/biosoftware/bppsuite/build/lib/libbpp-phyl.a
--   shared lib: /opt/biosoftware/bppsuite/build/lib/libbpp-phyl.so.12.0.0
--   includes: /opt/biosoftware/bppsuite/build/include
-- bpp-popgen 8.0.0 found:
--   static lib: /opt/biosoftware/bppsuite/build/lib/libbpp-popgen.a
--   shared lib: /opt/biosoftware/bppsuite/build/lib/libbpp-popgen.so.8.0.0
--   includes: /opt/biosoftware/bppsuite/build/include
-- makeinfo program not found: 'info' and 'html' target disabled (builds info/html doc)
-- Configuring done
CMake Warning (dev) at CMakeLists.txt:122 (ADD_DEPENDENCIES):
  Policy CMP0046 is not set: Error on non-existent dependency in
  add_dependencies.  Run "cmake --help-policy CMP0046" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  The dependency target "info" of target "rpm" does not exist.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /opt/biosoftware/bppsuite-3.0.0

Scanning dependencies of target bppml
[  2%] Building CXX object bppSuite/CMakeFiles/bppml.dir/bppML.cpp.o
/opt/biosoftware/bppsuite-3.0.0/bppSuite/bppML.cpp:58:10: fatal error: Bpp/Phyl/App/BppPhylogeneticsApplication.h: No such file or directory
   58 | #include <Bpp/Phyl/App/BppPhylogeneticsApplication.h>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [bppSuite/CMakeFiles/bppml.dir/build.make:63: bppSuite/CMakeFiles/bppml.dir/bppML.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:215: bppSuite/CMakeFiles/bppml.dir/all] Error 2
make: *** [Makefile:152: all] Error 2

Please could you add to your README.md file so that one knows the dependencies and might help resolving how to install the latest version?

Best regards

Kristian Ullrich

bppPopStats: wrong ancestral reconstruction with subsampling

While subsampling of the ingroup should only be used to estimate kappa and omega, it is also used to estimate the ancestral allele.

bppsuite - manual

Could you please change for the bpppopstats program one doc option.

In the manual it is written CodonSitesStatistics, however it seems to be spelled CodonSiteStatistics

https://github.com/BioPP/bppsuite/blob/master/doc/bppsuite.texi

@item CodonSitesStatistics
Generate a table with codon-site specifics statistics, including:

into

@item CodonSiteStatistics
Generate a table with codon-site specifics statistics, including:

Thank you in anticipation

Best regards

Kristian Ullrich

Bug with multiple outgroup sequences

bppPopStats does not output divergence values in the CodonSiteStatistics when more than one outgroup sequence is provided.

undefined symbol

Hi,

I have installed the bppsuite and its dependencies (bpp-core, bpp-seq, bpp-phyl, bpp-popgen) in a non standard path at CenOS. All of these libraries were downloaded by hand instead of using git clone, as this sever cannot access github. No error was reported during the make and installation.

However, when I run bppml for test, I got the error below:

$ ./bppml
./bppml: symbol lookup error: /lib64/libbpp-phyl3.so.1: undefined symbol: _ZN3bpp22AbstractParametrizable12setNamespaceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE

I guess that the CMake Warning is related to this issue. Could you please help me with this problem? Thanks in adavance.

cd bppsuite-master
cmake -DCMAKE_INSTALL_PREFIX=/share/software/BioPP/
CMake Warning:
  No source or binary directory provided.  Both will be assumed to be the
  same as the current working directory, but note that this warning will
  become a fatal error in future CMake releases.


-- Found /usr/bin/gzip compression program, using file extension .gz
-- bpp-core3 1.0.0 found:
--   static lib: not built/installed
--   shared lib: /share/software/BioPP/lib64/libbpp-core3.so.1.0.0
--   includes: /share/software/BioPP/include
-- bpp-seq3 1.0.0 found:
--   static lib: not built/installed
--   shared lib: /share/software/BioPP/lib64/libbpp-seq3.so.1.0.0
--   includes: /share/software/BioPP/include
-- bpp-phyl3 1.0.0 found:
--   static lib: not built/installed
--   shared lib: /share/software/BioPP/lib64/libbpp-phyl3.so.1.0.0
--   includes: /share/software/BioPP/include
-- bpp-popgen3 1.0.0 found:
--   static lib: not built/installed
--   shared lib: /share/software/BioPP/lib64/libbpp-popgen3.so.1.0.0
--   includes: /share/software/BioPP/include
-- Found /usr/bin/makeinfo: 'info' and 'html' target enabled (builds info/html doc)
-- Configuring done
-- Generating done
-- Build files have been written to: /share/software/BioPP/bppsuite-master

Kind regards,
Xiaojun

sth wrong with Bpp/Version.h when installing

Sorry, I met the mistakes when I compile the software, how can I make it?

[ 3%] Building CXX object CMakeFiles/bppml.dir/bppML.o
/public/home/Wanggs/software/bppsuite-master/bppSuite/bppML.cpp:13:10: fatal error: Bpp/Version.h: No such file or directory
13 | #include <Bpp/Version.h>
| ^~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/bppml.dir/bppML.o] Error1
make[1]: *** [CMakeFiles/bppml.dir/all] Error 2
make: *** [all] Error 2

Bug with fully unresolved sites

In bppPopStats, site output sends an exception in case a site with unresolved characters only is encountered.

Building bppSeqGen fails

make is failing to build bppSeqGen for me with the below output, with bpp-core etc. cloned and built from the main branches. Are these currently incompatible?

Thanks!
Claudia

  [ 28%] Building CXX object bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o
/software/bpp/bppsuite/bppSuite/bppSeqGen.cpp: In function ‘int main(int, char**)’:
/software/bpp/bppsuite/bppSuite/bppSeqGen.cpp:226:71: error: no matching function for call to ‘bpp::RandomTools::pickOne<std::__cxx11::string>(const std::vector<std::__cxx11::basic_string<char> >&, std::vector<double, std::allocator<double> >&)’
           auto pchar = RandomTools::pickOne<string>(resChar, probstate);
                                                                       ^
In file included from /software/bpp/include/Bpp/Seq/SequenceTools.h:47:0,
                 from /software/bpp/bppsuite/bppSuite/bppSeqGen.cpp:54:
/software/bpp/include/Bpp/Numeric/Random/RandomTools.h:185:12: note: candidate: template<class T> static T bpp::RandomTools::pickOne(std::vector<T>&, bool)
   static T pickOne(std::vector<T>& v, bool replace = false)
            ^~~~~~~
/software/bpp/include/Bpp/Numeric/Random/RandomTools.h:185:12: note:   template argument deduction/substitution failed:
/software/bpp/bppsuite/bppSuite/bppSeqGen.cpp:226:53: note:   cannot convert ‘resChar’ (type ‘const std::vector<std::__cxx11::basic_string<char> >’) to type ‘std::vector<std::__cxx11::basic_string<char> >&’
           auto pchar = RandomTools::pickOne<string>(resChar, probstate);
                                                     ^~~~~~~
In file included from /software/bpp/include/Bpp/Seq/SequenceTools.h:47:0,
                 from /software/bpp/bppsuite/bppSuite/bppSeqGen.cpp:54:
/software/bpp/include/Bpp/Numeric/Random/RandomTools.h:202:12: note: candidate: template<class T> static T bpp::RandomTools::pickOne(const std::vector<T>&)
   static T pickOne(const std::vector<T>& v)
            ^~~~~~~
/software/bpp/include/Bpp/Numeric/Random/RandomTools.h:202:12: note:   template argument deduction/substitution failed:
/software/bpp/bppsuite/bppSuite/bppSeqGen.cpp:226:71: note:   candidate expects 1 argument, 2 provided
           auto pchar = RandomTools::pickOne<string>(resChar, probstate);
                                                                       ^
In file included from /software/bpp/include/Bpp/Seq/SequenceTools.h:47:0,
                 from /software/bpp/bppsuite/bppSuite/bppSeqGen.cpp:54:
/software/bpp/include/Bpp/Numeric/Random/RandomTools.h:259:12: note: candidate: template<class T> static T bpp::RandomTools::pickOne(std::vector<T>&, std::vector<double, std::allocator<double> >&, bool)
   static T pickOne(std::vector<T>& v, std::vector<double>& w, bool replace = false)
            ^~~~~~~
/software/bpp/include/Bpp/Numeric/Random/RandomTools.h:259:12: note:   template argument deduction/substitution failed:
/software/bpp/bppsuite/bppSuite/bppSeqGen.cpp:226:53: note:   cannot convert ‘resChar’ (type ‘const std::vector<std::__cxx11::basic_string<char> >’) to type ‘std::vector<std::__cxx11::basic_string<char> >&’
           auto pchar = RandomTools::pickOne<string>(resChar, probstate);
                                                     ^~~~~~~
bppSuite/CMakeFiles/bppseqgen.dir/build.make:62: recipe for target 'bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o' failed
make[2]: *** [bppSuite/CMakeFiles/bppseqgen.dir/bppSeqGen.cpp.o] Error 1
CMakeFiles/Makefile2:358: recipe for target 'bppSuite/CMakeFiles/bppseqgen.dir/all' failed
make[1]: *** [bppSuite/CMakeFiles/bppseqgen.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2

biopp / bppsuite Goto Github PK

bppsuite's People

Stargazers

Watchers

Forkers

bppsuite's Issues

bppseqgen GTR model parameters

CodonSiteStatistics - output.file

bppseqgen expected to ignore branch length from root to mrca?

bppsuite 3.0.0 relies on not yet published bpp-phyl

compilation error - v3

bppPopStats: wrong ancestral reconstruction with subsampling

bppsuite - manual

Bug with multiple outgroup sequences

undefined symbol

sth wrong with Bpp/Version.h when installing

Bug with fully unresolved sites

Building bppSeqGen fails

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent