Source code for pytadbit

from future import standard_library
standard_library.install_aliases()
from os import environ
from subprocess import Popen, PIPE, check_call, CalledProcessError

from pytadbit._version import __version__

# ## Check if we have X display http://stackoverflow.com/questions/8257385/automatic-detection-of-display-availability-with-matplotlib
# if not "DISPLAY" in environ:
#     import matplotlib
#     matplotlib.use('Agg')
# else:
#     try:
#         check_call('python -c "import matplotlib.pyplot as plt; plt.figure()"',
#                    shell=True, stdout=PIPE, stderr=PIPE)
#     except CalledProcessError:
#         import matplotlib
#         matplotlib.use('Agg')

def get_dependencies_version(dico=False):
    """
    Check versions of TADbit and all dependencies, as well and retrieves system
    info. May be used to ensure reproducibility.

    :returns: string with description of versions installed
    """
    versions = {'  TADbit': __version__ + '\n\n'}
    try:
        import IMP
        try:
            versions['IMP'] = IMP.get_module_version()
            IMP.random_number_generator.seed(1)
            seed = IMP.random_number_generator()
        except AttributeError:
            versions['IMP'] = IMP.kernel.get_module_version()
            IMP.kernel.random_number_generator.seed(1)
            seed = IMP.kernel.random_number_generator()
        versions['IMP'] += ' (random seed indexed at 1 = %s)' % (seed)
    except ImportError:
        pass
        #  versions['IMP'] = 'Not found'
    try:
        import scipy
        versions['scipy'] = scipy.__version__
    except ImportError:
        versions['scipy'] = 'Not found'
    try:
        from gem import commands
        versions['gemtools'] = commands.__VERSION__
    except:
        versions['gemtools'] = 'Not found'
    try:
        from gem import executables
        out = Popen(executables['gem-mapper'], shell=True, stdout=PIPE,
                    stderr=PIPE, universal_newlines=True).communicate()
        versions['gem-mapper'] = out[1].split(' - ')[0].split('build ')[1]
    except:
        versions['gem-mapper'] = 'Not found'
    try:
        import numpy
        versions['numpy'] = numpy.__version__
    except ImportError:
        versions['numpy'] = 'Not found'
    try:
        import matplotlib
        versions['matplotlib'] = matplotlib.__version__
    except ImportError:
        versions['matplotlib'] = 'Not found'
    try:
        mcl, _ = Popen(['mcl', '--version'], stdout=PIPE,
                         stderr=PIPE, universal_newlines=True).communicate()
        versions['MCL'] = mcl.split()[1]
    except:
        versions['MCL'] = 'Not found'
    # try:
    #     chi, err = Popen(['chimera', '--version'], stdout=PIPE,
    #                      stderr=PIPE).communicate()
    #     versions['Chimera'] = chi.strip()
    # except:
    #     versions['Chimera'] = 'Not found'
    # try:
    #     chi, err = Popen(['chimera', '--version'], stdout=PIPE,
    #                      stderr=PIPE).communicate()
    #     versions['Chimera'] = chi.strip()
    # except:
    #     versions['Chimera'] = 'Not found'
    try:
        uname, err = Popen(['uname', '-rom'], stdout=PIPE,
                           stderr=PIPE, universal_newlines=True).communicate()
        versions[' Machine'] = uname
    except:
        versions[' Machine'] = 'Not found'

    if dico:
        return versions
    else:
        return '\n'.join(['%15s : %s' % (k, versions[k]) for k in
                          sorted(versions.keys())])


from pytadbit.hic_data                   import HiC_data
from pytadbit.tadbit                     import tadbit, batch_tadbit
from pytadbit.chromosome                 import Chromosome
from pytadbit.experiment                 import Experiment, load_experiment_from_reads
from pytadbit.chromosome                 import load_chromosome
from pytadbit.modelling.structuralmodels import StructuralModels
from pytadbit.modelling.structuralmodels import load_structuralmodels
from pytadbit.parsers.hic_parser         import load_hic_data_from_reads
from pytadbit.parsers.hic_parser         import load_hic_data_from_bam
from pytadbit.modelling.impmodel         import load_impmodel_from_cmm
from pytadbit.modelling.impmodel         import load_impmodel_from_xyz
from pytadbit.modelling.impmodel         import IMPmodel
from pytadbit.parsers.hic_parser         import read_matrix
try:
    from pytadbit.modelling.impoptimizer import IMPoptimizer
except ImportError:
    from warnings                  import warn
    # warn('IMP not found, check PYTHONPATH\n')