def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: cgat_make2help.py 2781 2009-09-10 11:33:14Z andreas $"
)
parser.add_option("-m",
"--method",
dest="method",
type="choice",
help="method to use [t-test=t-test]",
choices=("t-test", ))
parser.set_defaults(filename="Makefile", )
(options, args) = E.Start(parser, quiet=True, add_pipe_options=True)
src_dir = os.path.dirname(os.path.abspath(__file__))
makefiles = getMakefiles((options.filename, ),
source_directory=src_dir,
ignore_missing=True)
## variables starting with "PARAM"
parameters = {}
## main targets: no patterns or no dependencies
targets = []
## contain patterns and dependencies
rules = []
options.stdout.write("Help for makefile %s\n\n" %
os.path.abspath(options.filename))
options.stdout.write("""This file is organized in three sections.
1. Primary Targets
Primary targets are targets to be run by the users. Usually includes "all".
2. Parameters
Parameters defined in the makefile.
3. Secondary targets and rules
Rules defined in the makefile to build the primary targets.
""")
for makefile in makefiles:
infile = open(makefile, "r")
comment = []
last_line = None
first = True
for line in infile:
if last_line:
line = last_line + line
last_line = None
if not re.sub("\s+", "", line):
first = False
continue
if line[-2] == "\\":
last_line = line[:-2]
continue
if line[0] == "\t": continue
if line[0] == "#":
l = re.sub("^#+\s*", "", line[:-1])
if l and not first:
comment.append(l)
continue
x = re.match("(PARAM_\S+[^?:])\s*\?*\s*=(.+)", line)
if x:
param, value = x.groups()
if param not in parameters:
p = Parameter(param, comment, value)
parameters[param] = p
else:
p = parameters[param]
p.mComment += comment
p.mDefaultValue = value
x = re.match("(PARAM_\S+[^?])\s*=(.+)", line)
if x:
param, value = x.groups()
if param not in parameters:
p = Parameter(param, comment)
parameters[param] = p
else:
p = parameters[param]
p.mComment += comment
p.mValue = value
x = re.match("(\S+)\s*:\s*(.*)", line)
if x:
target, dependencies = x.groups()
if "=" in target or "=" in dependencies: continue
if target[0] in ".$": continue
if "hook" in target: continue
dependencies = re.sub("\s+", " ", dependencies)
if "." in target:
rules.append(Target(target, dependencies, comment))
else:
targets.append(Target(target, dependencies, comment))
comment = []
first = False
infile.close()
options.stdout.write("\n\n Section 1: Primary targets\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(
""" Primary targets are targets to be run by the users. Usually includes "all".\n\n"""
)
for x in targets:
options.stdout.write(x.printPretty() + "\n\n")
options.stdout.write("\n\n Section 2: Parameters\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(
""" A list of parameters defined in the makefile.\n\n""")
for x, y in sorted(parameters.items()):
options.stdout.write(y.printPretty() + "\n\n\n")
for x in targets:
options.stdout.write(x.printPretty() + "\n\n")
options.stdout.write("\n\n Section 3: Secondary targets and rules\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(""" Secondary targets are run by the pipeline.\n\n""")
for x in rules:
options.stdout.write(x.printPretty() + "\n\n")
options.stdout.write("\n\n Section 4: Contents\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(
" This help was created by scanning the contents of the following makefiles.\n"
)
for makefile in makefiles:
options.stdout.write(" %s\n" % makefile)
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id: cgat_make2help.py 2781 2009-09-10 11:33:14Z andreas $")
parser.add_option("-m", "--method", dest="method", type="choice",
help="method to use [t-test=t-test]",
choices=("t-test", ))
parser.set_defaults(
filename="Makefile",
)
(options, args) = E.Start(parser,
quiet=True,
add_pipe_options=True)
src_dir = os.path.dirname(os.path.abspath(__file__))
makefiles = getMakefiles(
(options.filename,), source_directory=src_dir, ignore_missing=True)
# variables starting with "PARAM"
parameters = {}
# main targets: no patterns or no dependencies
targets = []
# contain patterns and dependencies
rules = []
options.stdout.write("Help for makefile %s\n\n" %
os.path.abspath(options.filename))
options.stdout.write( """This file is organized in three sections.
1. Primary Targets
Primary targets are targets to be run by the users. Usually includes "all".
2. Parameters
Parameters defined in the makefile.
3. Secondary targets and rules
Rules defined in the makefile to build the primary targets.
""")
for makefile in makefiles:
infile = open(makefile, "r")
comment = []
last_line = None
first = True
for line in infile:
if last_line:
line = last_line + line
last_line = None
if not re.sub("\s+", "", line):
first = False
continue
if line[-2] == "\\":
last_line = line[:-2]
continue
if line[0] == "\t":
continue
if line[0] == "#":
l = re.sub("^#+\s*", "", line[:-1])
if l and not first:
comment.append(l)
continue
x = re.match("(PARAM_\S+[^?:])\s*\?*\s*=(.+)", line)
if x:
param, value = x.groups()
if param not in parameters:
p = Parameter(param, comment, value)
parameters[param] = p
else:
p = parameters[param]
p.mComment += comment
p.mDefaultValue = value
x = re.match("(PARAM_\S+[^?])\s*=(.+)", line)
if x:
param, value = x.groups()
if param not in parameters:
p = Parameter(param, comment)
parameters[param] = p
else:
p = parameters[param]
p.mComment += comment
p.mValue = value
x = re.match("(\S+)\s*:\s*(.*)", line)
if x:
target, dependencies = x.groups()
if "=" in target or "=" in dependencies:
continue
if target[0] in ".$":
continue
if "hook" in target:
continue
dependencies = re.sub("\s+", " ", dependencies)
if "." in target:
rules.append(Target(target, dependencies, comment))
else:
targets.append(Target(target, dependencies, comment))
comment = []
first = False
infile.close()
options.stdout.write("\n\n Section 1: Primary targets\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(
""" Primary targets are targets to be run by the users. Usually includes "all".\n\n""")
for x in targets:
options.stdout.write(x.printPretty() + "\n\n")
options.stdout.write("\n\n Section 2: Parameters\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(
""" A list of parameters defined in the makefile.\n\n""")
for x, y in sorted(parameters.items()):
options.stdout.write(y.printPretty() + "\n\n\n")
for x in targets:
options.stdout.write(x.printPretty() + "\n\n")
options.stdout.write("\n\n Section 3: Secondary targets and rules\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(""" Secondary targets are run by the pipeline.\n\n""")
for x in rules:
options.stdout.write(x.printPretty() + "\n\n")
options.stdout.write("\n\n Section 4: Contents\n")
options.stdout.write(" --------------------------\n\n")
options.stdout.write(
" This help was created by scanning the contents of the following makefiles.\n")
for makefile in makefiles:
options.stdout.write(" %s\n" % makefile)
E.Stop()
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser( version = "%prog version: $Id: gpipe/export_code.py 2781 2009-09-10 11:33:14Z andreas $")
parser.add_option("-t", "--tool-set", dest="tool_set",
help="set to use.", type="choice",
choices=("geneprediction", "codonbias", "geneprediction",
"codeml_benchmark" ) )
parser.add_option( "--test", dest="test", action = "store_true",
help = "testing mode [%default]" )
parser.add_option( "--release", dest="version", type="string",
help = "the version string [%default]" )
parser.set_defaults(
tool_set = "geneprediction",
libdirs = ("/home/andreas/cgat/", ),
scriptdirs = ("/home/andreas/cgat/", ),
name = None,
version = "0.0.1",
test = False,
)
(options, args) = E.Start( parser )
source_directory = os.path.realpath(os.path.dirname(sys.argv[0])) + "/"
if options.tool_set == "geneprediction":
makefiles = set( ("Makefile.gpipe",) )
method = "gpipe"
readme = README_GPIPE
if options.name == None: options.name = "gpipe"
elif os.path.exists( "%s/Makefile.%s" % (source_directory, options.tool_set) ):
makefiles = set( ("Makefile.%s" % options.tool_set,) )
method = options.tool_set
readme = README_GENERIC
if options.name == None: options.name = options.tool_set
else:
raise ValueError( "unknown toolset %s" % options.tool_set)
if options.test:
tmp_dir = "tmp"
os.mkdir(tmp_dir)
else:
tmp_dir = tempfile.mkdtemp()
nmissed_makefiles, nmissed_scripts, nmissed_modules = 0, 0, 0
makefiles = getMakefiles( makefiles, os.path.join( source_directory, "makefiles" ) )
target_directory= "%s/%s-%s/makefiles/" % ( tmp_dir, options.name, options.version )
os.makedirs( target_directory )
for makefile in makefiles:
src = os.path.join( source_directory, makefile )
if os.path.exists( src ):
shutil.copy( src, target_directory )
E.info( "makefile added: %s" % makefile )
else:
E.warn( "makefile missed: %s" % makefile )
nmissed_makefiles += 1
scripts = getScripts( makefiles, source_directory )
target_directory= "%s/%s-%s/" % ( tmp_dir, options.name, options.version )
modules = set()
for language, script in scripts:
## remove any path name variables
script = os.path.basename( script )
script = script[script.find(")")+1:]
for d in (source_directory,) + options.scriptdirs:
src = os.path.join( source_directory, script )
if os.path.exists( src ):
shutil.copy( src, target_directory )
if language == "python":
modules.add( script )
E.info( "script added: %s from %s" % (script, dir) )
break
else:
E.warn( "script missed: %s" % (script) )
nmissed_scripts += 1
modules, system_modules = getModules( modules,
(source_directory,) + options.scriptdirs,
options.libdirs )
for lib in modules:
## remove any path name variables
for dir in (source_directory,) + options.scriptdirs + options.libdirs:
if os.path.exists( dir + lib ):
shutil.copy( dir + lib,
target_directory + lib )
if options.loglevel >= 1:
options.stdout.write("module added: %s from %s\n" % (lib, dir) )
break
else:
if options.loglevel >= 1:
options.stdout.write("module missed: %s\n" % (lib) )
nmissed_scripts += 1
## Writing setup check file
outfile = open( target_directory + "check_gpipe/setup.py", "w")
for module in system_modules:
outfile.write("import %s\n" % module[:-3] )
outfile.write("print 'check successfull - all python modules required are present.'\n")
outfile.close()
## Writing setup file.
outfile = open( target_directory + "gpipe/setup.py", "w")
infile = open( source_directory + "gpipe/setup.py" )
for line in infile:
if re.search("method = None", line):
line = line[line.find(method):] + "method = '%s',\n" % method
outfile.write(line)
outfile.close()
## Writing the README file
params = { 'dir':"%s-%s" % (options.name, options.version),
}
outfile = open( target_directory + "README", "w")
outfile.write( PREAMBL + "\n" )
outfile.write( README_INSTALLATION % params + "\n")
outfile.write( readme % params + "\n" )
outfile.close()
## Wrap the whole thing up
os.system( "tar -C %s -czf %s/%s-%s.tgz %s-%s" % (tmp_dir, tmp_dir, options.name, options.version,
options.name, options.version, ) )
E.info( "nmissed: makefiles=%i, scripts=%i, modules=%i" % (nmissed_makefiles, nmissed_scripts, nmissed_modules ) )
if not options.test:
shutil.copy( "%s/%s-%s.tgz" % (tmp_dir, options.name, options.version) , "." )
shutil.rmtree( tmp_dir )
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: gpipe/export_code.py 2781 2009-09-10 11:33:14Z andreas $"
)
parser.add_option("-t",
"--tool-set",
dest="tool_set",
help="set to use.",
type="choice",
choices=("geneprediction", "codonbias", "geneprediction",
"codeml_benchmark"))
parser.add_option("--test",
dest="test",
action="store_true",
help="testing mode [%default]")
parser.add_option("--release",
dest="version",
type="string",
help="the version string [%default]")
parser.set_defaults(
tool_set="geneprediction",
libdirs=("/home/andreas/cgat/", ),
scriptdirs=("/home/andreas/cgat/", ),
name=None,
version="0.0.1",
test=False,
)
(options, args) = E.Start(parser)
source_directory = os.path.realpath(os.path.dirname(sys.argv[0])) + "/"
if options.tool_set == "geneprediction":
makefiles = set(("Makefile.gpipe", ))
method = "gpipe"
readme = README_GPIPE
if options.name is None:
options.name = "gpipe"
elif os.path.exists("%s/Makefile.%s" %
(source_directory, options.tool_set)):
makefiles = set(("Makefile.%s" % options.tool_set, ))
method = options.tool_set
readme = README_GENERIC
if options.name is None:
options.name = options.tool_set
else:
raise ValueError("unknown toolset %s" % options.tool_set)
if options.test:
tmp_dir = "tmp"
os.mkdir(tmp_dir)
else:
tmp_dir = tempfile.mkdtemp()
nmissed_makefiles, nmissed_scripts, nmissed_modules = 0, 0, 0
makefiles = getMakefiles(makefiles,
os.path.join(source_directory, "makefiles"))
target_directory = "%s/%s-%s/makefiles/" % (tmp_dir, options.name,
options.version)
os.makedirs(target_directory)
for makefile in makefiles:
src = os.path.join(source_directory, makefile)
if os.path.exists(src):
shutil.copy(src, target_directory)
E.info("makefile added: %s" % makefile)
else:
E.warn("makefile missed: %s" % makefile)
nmissed_makefiles += 1
scripts = getScripts(makefiles, source_directory)
target_directory = "%s/%s-%s/" % (tmp_dir, options.name, options.version)
modules = set()
for language, script in scripts:
# remove any path name variables
script = os.path.basename(script)
script = script[script.find(")") + 1:]
for d in (source_directory, ) + options.scriptdirs:
src = os.path.join(source_directory, script)
if os.path.exists(src):
shutil.copy(src, target_directory)
if language == "python":
modules.add(script)
E.info("script added: %s from %s" % (script, dir))
break
else:
E.warn("script missed: %s" % (script))
nmissed_scripts += 1
modules, system_modules = getModules(modules, (source_directory, ) +
options.scriptdirs, options.libdirs)
for lib in modules:
# remove any path name variables
for dir in (source_directory, ) + options.scriptdirs + options.libdirs:
if os.path.exists(dir + lib):
shutil.copy(dir + lib, target_directory + lib)
if options.loglevel >= 1:
options.stdout.write("module added: %s from %s\n" %
(lib, dir))
break
else:
if options.loglevel >= 1:
options.stdout.write("module missed: %s\n" % (lib))
nmissed_scripts += 1
# Writing setup check file
outfile = open(target_directory + "check_gpipe/setup.py", "w")
for module in system_modules:
outfile.write("import %s\n" % module[:-3])
outfile.write(
"print 'check successfull - all python modules required are present.'\n"
)
outfile.close()
# Writing setup file.
outfile = open(target_directory + "gpipe/setup.py", "w")
infile = open(source_directory + "gpipe/setup.py")
for line in infile:
if re.search("method = None", line):
line = line[line.find(method):] + "method = '%s',\n" % method
outfile.write(line)
outfile.close()
# Writing the README file
params = {
'dir': "%s-%s" % (options.name, options.version),
}
outfile = open(target_directory + "README", "w")
outfile.write(PREAMBL + "\n")
outfile.write(README_INSTALLATION % params + "\n")
outfile.write(readme % params + "\n")
outfile.close()
# Wrap the whole thing up
os.system("tar -C %s -czf %s/%s-%s.tgz %s-%s" % (
tmp_dir,
tmp_dir,
options.name,
options.version,
options.name,
options.version,
))
E.info("nmissed: makefiles=%i, scripts=%i, modules=%i" %
(nmissed_makefiles, nmissed_scripts, nmissed_modules))
if not options.test:
shutil.copy("%s/%s-%s.tgz" % (tmp_dir, options.name, options.version),
".")
shutil.rmtree(tmp_dir)
E.Stop()
makefiles = set( ("Makefile.%s" % options.tool_set,) )
method = options.tool_set
readme = README_GENERIC
if options.name == None: options.name = options.tool_set
else:
raise ValueError( "unknown toolset %s" % options.tool_set)
if options.test:
tmp_dir = "tmp"
os.mkdir(tmp_dir)
else:
tmp_dir = tempfile.mkdtemp()
nmissed_makefiles, nmissed_scripts, nmissed_modules = 0, 0, 0
makefiles = getMakefiles( makefiles, os.path.join( source_directory, "makefiles" ) )
target_directory= "%s/%s-%s/makefiles/" % ( tmp_dir, options.name, options.version )
os.makedirs( target_directory )
for makefile in makefiles:
src = os.path.join( source_directory, makefile )
if os.path.exists( src ):
shutil.copy( src, target_directory )
E.info( "makefile added: %s" % makefile )
else:
E.warn( "makefile missed: %s" % makefile )
nmissed_makefiles += 1
scripts = getScripts( makefiles, source_directory )
