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Consider the following ipython session:

$ ipython3
Python 3.6.0 (default, Feb  8 2017, 15:44:49) 
Type 'copyright', 'credits' or 'license' for more information
IPython 6.2.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from gatb import Bank

In [2]: b = Bank("this_file/does_not/exist")
terminate called after throwing an instance of 'gatb::core::system::Exception'
Aborted (core dumped)

Would it be possible to have an exception raised instead of a crash, or would this severely affect performances ?

Hello,

I was running setup.py and an error raised in test_graph.py, any advices ? Below the result from setup.py :

~/pyGATB/build$ python3 setup.py test
running pytest
Searching for pytest
Best match: pytest 3.5.0
Processing pytest-3.5.0-py3.5.egg

Using /home/jeanjean/pyGATB/build/.eggs/pytest-3.5.0-py3.5.egg
Searching for py>=1.5.0
Best match: py 1.5.3
Processing py-1.5.3-py3.5.egg

Using /home/jeanjean/pyGATB/build/.eggs/py-1.5.3-py3.5.egg
Searching for pluggy<0.7,>=0.5
Best match: pluggy 0.6.0
Processing pluggy-0.6.0-py3.5.egg

Using /home/jeanjean/pyGATB/build/.eggs/pluggy-0.6.0-py3.5.egg
Searching for more-itertools>=4.0.0
Best match: more-itertools 4.1.0
Processing more_itertools-4.1.0-py3.5.egg

Using /home/jeanjean/pyGATB/build/.eggs/more_itertools-4.1.0-py3.5.egg
Searching for attrs>=17.4.0
Best match: attrs 17.4.0
Processing attrs-17.4.0-py3.5.egg

Using /home/jeanjean/pyGATB/build/.eggs/attrs-17.4.0-py3.5.egg
running egg_info
creating pyGATB.egg-info
writing pyGATB.egg-info/PKG-INFO
writing dependency_links to pyGATB.egg-info/dependency_links.txt
writing top-level names to pyGATB.egg-info/top_level.txt
writing requirements to pyGATB.egg-info/requires.txt
writing manifest file 'pyGATB.egg-info/SOURCES.txt'
reading manifest file 'pyGATB.egg-info/SOURCES.txt'
writing manifest file 'pyGATB.egg-info/SOURCES.txt'
running build_ext
============================== test session starts =====================
platform linux -- Python 3.5.2, pytest-3.5.0, py-1.5.3, pluggy-0.6.0
rootdir: /home/jeanjean/pyGATB/build, inifile: setup.cfg
collected 17 items

src/tests/test_bank.py ....... [ 41%]
src/tests/test_graph.py .Aborted (core dumped)

Then trying to load h5 in ipython to test Graph module i got the same error :

Python 3.5.2 (default, Nov 23 2017, 16:37:01)
Type 'copyright', 'credits' or 'license' for more information
IPython 6.3.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from gatb import Graph
In [2]: graph=Graph('-in ../thirdparty/gatb-core/gatb-core/test/db/celegans_reads.h5')
Input is h5 or _gatb/ (we assume that kmer counting has already been done), we will complete it into a graph if necessary.
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)

I just tried the fasta parsing feature of pyGATB, and I find surprizing results. See the following ipython3 session:

In [1]: from gatb import Bank

In [2]: sum(len(seq.sequence) for seq in Bank("/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"))
Out[2]: 102932909

In [3]: sum((len(line.strip()) for line in open("/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa") if line[0] != ">"))
Out[3]: 100286401

What could explain the differences ?

Edit: Same issue with the provided example:

In [1]: from gatb import Bank

In [2]: sum(len(seq.sequence) for seq in Bank("/home/bli/src/pyGATB/thirdparty/gatb-core/gatb-core/test/db/query.fa"))
Out[2]: 40428

In [3]: sum((len(line.strip()) for line in open("/home/bli/src/pyGATB/thirdparty/gatb-core/gatb-core/test/db/query.fa") if line[0] != ">"))
Out[3]: 39699

Hello, I installed pyGATB using pip and python v3.5.6 on our cluster. I was playing around with the data and while I could reproduce the sample code for the Bank module, the code kept causing a segmentation fault when I tried to read the data into Graph (whether it was a h5 or fastq file):

~/gatbTest$ python
Python 3.5.6 |Anaconda, Inc.| (default, Aug 26 2018, 21:41:56) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from gatb import Graph
>>> graph = Graph('-in ./celegans_reads.h5')
Input is h5 or _gatb/ (we assume that kmer counting has already been done), we will complete it into a graph if necessary.
Segmentation fault
~/gatbTest$ python
Python 3.5.6 |Anaconda, Inc.| (default, Aug 26 2018, 21:41:56) 
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from gatb import Graph
>>> graph = Graph('-in ./colombaTestBig_R2.fq')
Segmentation fault

On OSX, I did:

cd <some_fresh_dir>
git clone https://github.com/GATB/pyGATB.git
mkdir build ; cd build;
cmake -DCMAKE_BUILD_TYPE=Release ..

While checking at the CMale working trace, I saw this:

-- Found PythonInterp: /Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4 (found version "3.4.4") 
-- Found Cython: /Library/Frameworks/Python.framework/Versions/3.4/bin/cython  
-- Found PythonLibs: /usr/lib/libpython2.7.dylib (found version "2.7.10") 

Where there is the problem: PythonInterp 3.4.4 vs. PythonLibs 2.7.10.

How can we fix that?