jheled / biopy Goto Github PK
View Code? Open in Web Editor NEWAutomatically exported from code.google.com/p/biopy
Automatically exported from code.google.com/p/biopy
*What steps will reproduce the problem?*
Running summary_tree script on a BEAST nexus trees file.
*What is the expected output? What do you see instead?*
counting trees ..., reading 9000 trees ...,Traceback (most recent call last):
File "./summary_tree", line 98, in <module>
trees = list(nexusReader.read(nexFile, slice(int(burnIn*nTrees), -1, every)))
File "/usr/local/lib/python2.7/dist-packages/biopy/INexus.py", line 591, in read
for i in ii:
File "/usr/local/lib/python2.7/dist-packages/biopy/INexus.py", line 635, in _parse_nexus_block
for i in ii:
File "/usr/local/lib/python2.7/dist-packages/biopy/INexus.py", line 943, in _tree
rooted=rooted, name=name)
File "/usr/local/lib/python2.7/dist-packages/biopy/parseNewick.py", line 153, in parseNewick
nodes = parsetree(txt)
ValueError: failed parsing.
I inspected the newick string in the "parsetree(txt)"-- it is failing on the
first tree in the nexus file. The tree seems to be formatted correctly.
What version of the product are you using? On what operating system?
Latest svn (march 26 2012).
Please provide any additional information below.
Installation did not have any errors, but there were a couple warnings:
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/lib/pymodules/python2.7/numpy/core/include
-I/usr/include/python2.7 -c biopy/cchelp.cc -o
build/temp.linux-i686-2.7/biopy/cchelp.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for
Ada/C/ObjC but not for C++ [enabled by default]
g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions
build/temp.linux-i686-2.7/biopy/cchelp.o -o build/lib.linux-i686-2.7/cchelp.so
building 'cnexus' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c biopy/cnexus.c -o
build/temp.linux-i686-2.7/biopy/cnexus.o
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions
build/temp.linux-i686-2.7/biopy/cnexus.o -o build/lib.linux-i686-2.7/cnexus.so
Original issue reported on code.google.com by [email protected]
on 27 Mar 2012 at 11:02
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.