old_contents: # ===========================================================================
  #   pyGATB : Python3 wrapper for GATB-Core
  #   Copyright (C) 2017 INRIA
  #   Author: Mael Kerbiriou
  #
  #  This program is free software: you can redistribute it and/or modify
  #  it under the terms of the GNU Affero General Public License as
  #  published by the Free Software Foundation, either version 3 of the
  #  License, or (at your option) any later version.
  #
  #  This program is distributed in the hope that it will be useful,
  #  but WITHOUT ANY WARRANTY; without even the implied warranty of
  #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  #  GNU Affero General Public License for more details.
  #
  #  You should have received a copy of the GNU Affero General Public License
  #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  # ===========================================================================
  
  # we import pyGATB Graph
  from gatb import Graph
  
  # We will use a file containing a De Bruijn Graph stored
  # in HDF5 format; file created using dbgh5 tool provided
  # with GATB-Core. (This file is located next to this snippet)
  F_NAME='../thirdparty/gatb-core/gatb-core/test/db/celegans_reads.h5'
  
  # We create the graph from our .h5 file
  # Note: Graph directly accepts Fasta or Fastq files
  graph = Graph('-in %s' % F_NAME)
  
  # We iterate over some nodes
  for i, node in enumerate(graph):
      print('{}: {!r}'.format(i, node))
      if i > 10: break
  
new_contents: # ===========================================================================
  #   pyGATB : Python3 wrapper for GATB-Core
  #   Copyright (C) 2017 INRIA
  #   Author: Mael Kerbiriou
  #
  #  This program is free software: you can redistribute it and/or modify
  #  it under the terms of the GNU Affero General Public License as
  #  published by the Free Software Foundation, either version 3 of the
  #  License, or (at your option) any later version.
  #
  #  This program is distributed in the hope that it will be useful,
  #  but WITHOUT ANY WARRANTY; without even the implied warranty of
  #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  #  GNU Affero General Public License for more details.
  #
  #  You should have received a copy of the GNU Affero General Public License
  #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  # ===========================================================================
  
  # we import pyGATB Graph
  from gatb import Graph
  
  # We will use a file containing a De Bruijn Graph stored
  # in HDF5 format; file created using dbgh5 tool provided
  # with GATB-Core. (This file is located next to this snippet)
  F_NAME='../thirdparty/gatb-core/gatb-core/test/db/celegans_reads.h5'
  
  # We create the graph from our .h5 file
  # Note: Graph also accepts Fasta or Fastq files
  graph = Graph('-in %s' % F_NAME)
  
  # We iterate over some nodes
  for i, node in enumerate(graph):
      print('{}: {!r}'.format(i, node))
      if i > 10: break
  
subject: Update read_h5.py