def main(module_path, class_name):
# Explicitly import module
# If class defined in __main__ module, pickles won't load
module = __import__(module_path, globals(), fromlist=True)
designer = getattr(module, class_name)()
args = sys.argv[1:]
config.shell_run(designer, args, sys.executable + ' -m ' + module_path)
def main(module_path, class_name):
# Explicitly import module
# If class defined in __main__ module, pickles won't load
module = __import__(module_path, globals(), fromlist=True)
designer = getattr(module, class_name)()
args = sys.argv[1:]
config.shell_run(designer, args, sys.executable + ' -m ' + module_path)
def run_toolbox(action_classes, script_name='', show_make_flags=True):
"""
Provide a command line interface for a list of Actions.
Note:
strings included in the action_classes list will be printed
as help text, for example to display section headings.
"""
args = configure_making(sys.argv[1:])
commands = { }
for item in action_classes:
if isinstance(item, str):
continue
name = item.shell_name()
commands[ name ] = item
if args == [ '--help-make' ]:
help = [ '\n' ]
help.append('\nMake options:\n'+Make().describe('', show_help=True, escape_newlines=False)+'\n')
config.write_colored_text(sys.stdout, ''.join(help)+'\n\n')
sys.exit(1)
if not args or args == ['-h'] or args == ['--help']:
help = [ '\n' ]
for item in action_classes:
if isinstance(item, str):
help.append(config.wrap(item, 70) + '\n\n')
continue
name = item.shell_name()
help.append(' %s\n' % config.colored(1,name+':'))
help.append(config.color_as_comment(config.wrap(item.help_short, 70, ' ')) + '\n\n')
if show_make_flags:
#help.append('\nMake options:\n'+Make().describe('', show_help=True, escape_newlines=False)+'\n')
help.append('\nFor workflow make options type "%s --help-make".\n' % script_name)
config.write_colored_text(sys.stdout, ''.join(help))
sys.exit(1)
try:
command, args = args[0], args[1:]
mangled_command = command.lower().rstrip(':')
if mangled_command not in commands:
raise grace.Error("Don't know how to "+command)
except:
config.report_exception()
sys.exit(1)
config.shell_run(commands[mangled_command](), args, (script_name+' ' if script_name else '') + mangled_command+':')
def run_script(function):
""" Run a workflow script. Various command line flags are parsed,
then any remaining command line parameters are passed to the
function.
Intended usage:
from nesoni import *
def my_script():
...
if __name__ == '__main__':
run_script(my_script)
"""
maker = Make_script(function=function)
config.shell_run(maker, sys.argv[1:], sys.executable + ' ' + sys.argv[0])
def run_script(function):
""" Run a workflow script. Various command line flags are parsed,
then any remaining command line parameters are passed to the
function.
Intended usage:
from nesoni import *
def my_script():
...
if __name__ == '__main__':
run_script(my_script)
"""
maker = Make_script(function=function)
config.shell_run(maker, sys.argv[1:], sys.executable + ' ' + sys.argv[0])
def run_toolbox(action_classes, script_name=''):
"""
Provide a command line interface for a list of Actions.
Note:
strings included in the action_classes list will be printed
as help text, for example to display section headings.
"""
commands = { }
help = [ '\n' ]
for item in action_classes:
if isinstance(item, str):
help.append(config.wrap(item, 70) + '\n\n')
continue
name = item.shell_name()
commands[ name ] = item
help.append(' %s\n' % config.colored(1,name+':'))
help.append(config.wrap(item.help_short, 70, ' ') + '\n\n')
args = sys.argv[1:]
if not args:
config.write_colored_text(sys.stdout, ''.join(help)+'\n\n')
sys.exit(1)
try:
command, args = args[0], args[1:]
mangled_command = command.lower().rstrip(':')
if mangled_command not in commands:
raise grace.Error("Don't know how to "+command)
except:
config.report_exception()
sys.exit(1)
config.shell_run(commands[mangled_command](), args, (script_name+' ' if script_name else '') + mangled_command+':')
if a_start > self.length:
if a_start < len(seq):
n_clipped += 1
total_clipped += a_start
print >> out_file, '@'+name
print >> out_file, seq[:a_start]
print >> out_file, '+'
print >> out_file, qual[:a_start]
else:
n_discarded += 1
if n%10000 == 0:
grace.status('Clip-runs ' + self.sample + ' ' + grace.pretty_number(n)) # + ' (' + grace.pretty_number(len(dstates)) + ' dstates)')
grace.status('')
self.log.datum(self.sample,'reads',n)
if n:
self.log.datum(self.sample,'mean length before poly-A/adaptor clipping',float(total_before)/n)
self.log.datum(self.sample,'reads discarded as too short after poly-A/adaptor clipping',n_discarded)
self.log.datum(self.sample,'reads poly-A/adaptor clipped and kept',n_clipped)
if n_clipped:
self.log.datum(self.sample,'mean length clipped',float(total_clipped)/n_clipped)
if __name__ == '__main__':
config.shell_run(Clip_runs(), sys.argv[1:], sys.executable + ' ' + __file__)
def run_tool(action_class):
"""
Provide a command line interface for an Action.
"""
args = configure_making(sys.argv[1:])
config.shell_run(action_class(), args, sys.argv[0])
def run_toolbox(action_classes, script_name='', show_make_flags=True):
"""
Provide a command line interface for a list of Actions.
Note:
strings included in the action_classes list will be printed
as help text, for example to display section headings.
"""
args = configure_making(sys.argv[1:])
commands = {}
for item in action_classes:
if isinstance(item, str):
continue
name = item.shell_name()
commands[name] = item
if args == ['--help-make']:
help = ['\n']
help.append(
'\nMake options:\n' +
Make().describe('', show_help=True, escape_newlines=False) + '\n')
config.write_colored_text(sys.stdout, ''.join(help) + '\n\n')
sys.exit(1)
if not args or args == ['-h'] or args == ['--help']:
help = ['\n']
for item in action_classes:
if isinstance(item, str):
help.append(config.wrap(item, 70) + '\n\n')
continue
name = item.shell_name()
help.append(' %s\n' % config.colored(1, name + ':'))
help.append(
config.color_as_comment(
config.wrap(item.help_short, 70, ' ')) + '\n\n')
if show_make_flags:
#help.append('\nMake options:\n'+Make().describe('', show_help=True, escape_newlines=False)+'\n')
help.append(
'\nFor workflow make options type "%s --help-make".\n' %
script_name)
config.write_colored_text(sys.stdout, ''.join(help))
sys.exit(1)
try:
command, args = args[0], args[1:]
mangled_command = command.lower().rstrip(':')
if mangled_command not in commands:
raise grace.Error("Don't know how to " + command)
except:
config.report_exception()
sys.exit(1)
config.shell_run(commands[mangled_command](), args,
(script_name + ' ' if script_name else '') +
mangled_command + ':')
def run_tool(action_class):
"""
Provide a command line interface for an Action.
"""
args = configure_making(sys.argv[1:])
config.shell_run(action_class(), args, sys.argv[0])
fq = io.open_possibly_compressed_file(self.qual_file)
out_file = self.begin_output()
while True:
a1 = fa.readline()
if not a1: break
a1 = a1.strip()
a2 = fa.readline().strip()
q1 = fq.readline().strip()
q2 = fq.readline().strip()
assert a1.startswith('>')
assert a1 == q1
print >> out_file, '@' + a1[1:]
print >> out_file, a2
print >> out_file, '+'
print >> out_file, ''.join(
chr(33 + max(0, int(item))) for item in q2.split())
self.end_output(out_file)
fa.close()
fq.close()
if __name__ == '__main__':
config.shell_run(Fasta_qual_merge(), sys.argv[1:],
sys.executable + ' ' + __file__)
fa = io.open_possibly_compressed_file(self.fasta_file)
fq = io.open_possibly_compressed_file(self.qual_file)
out_file = self.begin_output()
while True:
a1 = fa.readline()
if not a1:
break
a1 = a1.strip()
a2 = fa.readline().strip()
q1 = fq.readline().strip()
q2 = fq.readline().strip()
assert a1.startswith(">")
assert a1 == q1
print >> out_file, "@" + a1[1:]
print >> out_file, a2
print >> out_file, "+"
print >> out_file, "".join(chr(33 + max(0, int(item))) for item in q2.split())
self.end_output(out_file)
fa.close()
fq.close()
if __name__ == "__main__":
config.shell_run(Fasta_qual_merge(), sys.argv[1:], sys.executable + " " + __file__)
#if reverse:
# tail_refpos = al.pos-extension
#else:
# tail_refpos = al.pos+al.length+extension-1
#al.extra.append('AA:i:%d'%tail_refpos)
al.extra.append('AA:i:1')
cigar += 'M' * extension
read_bases += 'N' * extension #Since mispriming is so common (and loading the original sequence here would be a pain)
read_qual += chr(33 + 20) * extension #Arbitrarily give quality 20
al.length += extension
if reverse:
al.pos -= extension
al.seq = rev_comp(read_bases)
al.qual = read_qual[::-1]
al.cigar = cigar_encode(cigar[::-1])
else:
al.seq = read_bases
al.qual = read_qual
al.cigar = cigar_encode(cigar)
print >> out_file, al
self.end_output(out_file)
self.end_input(in_file)
if __name__ == '__main__':
config.shell_run(Extend_sam(), sys.argv[1:],
sys.executable + ' ' + __file__)
print >> out_file, '@'+name
print >> out_file, seq[:a_start]
print >> out_file, '+'
print >> out_file, qual[:a_start]
else:
n_discarded += 1
if n%10000 == 0:
grace.status('Clip-runs ' + self.sample + ' ' + grace.pretty_number(n)) # + ' (' + grace.pretty_number(len(dstates)) + ' dstates)')
# Option to do a quick subsample
if self.only and self.only <= n:
break
grace.status('')
self.log.datum(self.sample,'reads',n)
if n:
self.log.datum(self.sample,'mean length before poly-A/adaptor clipping',float(total_before)/n)
self.log.datum(self.sample,'reads discarded as too short after poly-A/adaptor clipping',n_discarded)
self.log.datum(self.sample,'reads poly-A/adaptor clipped and kept',n_clipped)
if n_clipped:
self.log.datum(self.sample,'mean length clipped',float(total_clipped)/n_clipped)
if __name__ == '__main__':
config.shell_run(Clip_runs(), sys.argv[1:], sys.executable + ' ' + __file__)
#if reverse:
# tail_refpos = al.pos-extension
#else:
# tail_refpos = al.pos+al.length+extension-1
#al.extra.append('AA:i:%d'%tail_refpos)
al.extra.append('AA:i:1')
cigar += 'M' * extension
read_bases += 'N' * extension #Since mispriming is so common (and loading the original sequence here would be a pain)
read_qual += chr(33+20) * extension #Arbitrarily give quality 20
al.length += extension
if reverse:
al.pos -= extension
al.seq = rev_comp(read_bases)
al.qual = read_qual[::-1]
al.cigar = cigar_encode(cigar[::-1])
else:
al.seq = read_bases
al.qual = read_qual
al.cigar = cigar_encode(cigar)
print >> out_file, al
self.end_output(out_file)
self.end_input(in_file)
if __name__ == '__main__':
config.shell_run(Extend_sam(), sys.argv[1:], sys.executable + ' ' + __file__)
def run_tool(action_class):
"""
Provide a command line interface for an Action.
"""
config.shell_run(action_class(), sys.argv[1:], sys.argv[0])
