# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker dannonbaker@me.com # Date 1289832899 18000 # Node ID 095dc06e0728556426a9288e6448fd1114e24063 # Parent 47d6c393f4cf9562e4e3e10211389f84bf0a2f24 Python 2.4 Compatibility Fix. ( with open():)
--- a/lib/galaxy/jobs/splitters/basic.py +++ b/lib/galaxy/jobs/splitters/basic.py @@ -3,17 +3,19 @@ log = logging.getLogger( __name__ )
def _file_len(fname): i = 0 - with open(fname) as f: - for i, l in enumerate(f): - pass + f = open(fname) + for i, l in enumerate(f): + pass + f.close() return i + 1
def _fq_seq_count(fname): count = 0 - with open(fname) as f: - for i, l in enumerate(f): - if l.startswith('@'): - count += 1 + f = open(fname) + for i, l in enumerate(f): + if l.startswith('@'): + count += 1 + f.close() return count
def split_fq(input_file, working_directory, parts): @@ -25,25 +27,27 @@ def split_fq(input_file, working_directo if length < parts: parts = length len_each, remainder = divmod(length, parts) - with open(input_file, 'rt') as f: - for p in range(0, parts): - part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) - if not os.path.exists( part_dir ): - os.mkdir( part_dir ) - part_path = os.path.join(part_dir, os.path.basename(input_file)) - with open(part_path, 'w') as part_file: - for l in range(0, len_each): - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - if remainder > 0: - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - remainder -= 1 - outputs.append(part_path) + f = open(input_file, 'rt') + for p in range(0, parts): + part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) + if not os.path.exists( part_dir ): + os.mkdir( part_dir ) + part_path = os.path.join(part_dir, os.path.basename(input_file)) + part_file = open(part_path, 'w') + for l in range(0, len_each): + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + if remainder > 0: + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + part_file.write(f.readline()) + remainder -= 1 + outputs.append(part_path) + part_file.close() + f.close() return outputs
def split_txt(input_file, working_directory, parts): @@ -52,19 +56,21 @@ def split_txt(input_file, working_direct if length < parts: parts = length len_each, remainder = divmod(length, parts) - with open(input_file, 'rt') as f: - for p in range(0, parts): - part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) - if not os.path.exists( part_dir ): - os.mkdir( part_dir ) - part_path = os.path.join(part_dir, os.path.basename(input_file)) - with open(part_path, 'w') as part_file: - for l in range(0, len_each): - part_file.write(f.readline()) - if remainder > 0: - part_file.write(f.readline()) - remainder -= 1 - outputs.append(part_path) + f = open(input_file, 'rt') + for p in range(0, parts): + part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) + if not os.path.exists( part_dir ): + os.mkdir( part_dir ) + part_path = os.path.join(part_dir, os.path.basename(input_file)) + part_file = open(part_path, 'w') + for l in range(0, len_each): + part_file.write(f.readline()) + if remainder > 0: + part_file.write(f.readline()) + remainder -= 1 + outputs.append(part_path) + part_file.close() + f.close() return outputs
def split( input_file, working_directory, parts, file_type = None):