def _run(runcmd, args=None, defaults=None, quiet=False, dryrun=False, **params):
"""
Returns the name of the outfile.
* cmd - name of the executable
* args - unmodified arguments appended to end of command line
* dryrun - build the command line and quit
* defaults - an optional dict of key=val parameters
* params - pass arguments as either key=val pairs, or as
key='' if key has no argument
"""
cmd = sequtil.find_exec(runcmd)
if cmd is None:
raise OSError('%s could not be found' % runcmd)
os_type = sequtil.get_os_type()
if os_type != 'POSIX':
raise OSError('Operating system must be POSIX-like')
if defaults is None:
defaults = {}
defaults.update(params)
arguments = [cmd]
for k,v in defaults.items():
if len(k) == 1:
dashes = '-'
else:
dashes = '--'
if v is None or not v.strip():
add = ['%(dashes)s%(k)s']
else:
add = ['%(dashes)s%(k)s', '%(v)s']
arguments.extend([fstr % locals() for fstr in add])
if args:
arguments.extend(args)
log.info(arguments)
log.info(' '.join(arguments))
if dryrun:
return None, None
else:
stdoutdata, stderrdata = subprocess.Popen(arguments, stdout=subprocess.PIPE).communicate()
if stderrdata:
log.error(stderrdata)
log.info(stdoutdata[:500])
if not quiet:
print stdoutdata
return stdoutdata, stderrdata
def run(target_file, clustal_cmd='clustalw', run=True, silent=False, **params):
"""Run clustalw -options for command line parameters"""
if sequtil.find_exec(clustal_cmd) is None:
raise OSError('%s could not be found' % clustal_cmd)
os_type = sequtil.get_os_type()
log.debug('os type is set as %s' % os_type)
# defaults = getparams(
# align=None,
# batch=None,
# infile=target_file,
# output='phylip',
# outputtree='nj')
target_file = os.path.abspath(target_file)
defaults = getparams(infile=target_file)
defaults.update(params)
args = []
args.append('"%s"'%clustal_cmd) # surround with quotes to accomodate spaces
if os_type == 'POSIX':
argchar='-'
elif os_type == 'WINDOWS':
argchar='/'
for k,v in defaults.items():
if v:
args.append('%s%s="%s"' % (argchar,k,v))
else:
args.append('%s%s' % (argchar,k))
if silent:
args.append('> %s' % os.devnull)
cmd = ' '.join(args)
log.info(cmd)
if run and os_type == 'POSIX':
log.info('running clustalw: %s' % cmd)
os.system( cmd )
elif os_type == 'WINDOWS':
cwd,_ = os.path.split(target_file)
cmds = ['cd "%s"' % cwd, cmd]
sequtil.run_bat(cmds, path=cwd, run=run)
return cmd
def run(hmmcmd, infile, outfile=False, dryrun=False, defaults=None, quiet=False, **params):
"""
Returns the name of the outfile.
* cmd - choose one of hmmalign hmmbuild hmmcalibrate
hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch
* infile - input file name
* outfile - optional output file name. If False, no output file
is specified; if None, output is written to a file given a random name.
* dryrun - build the command line and quit
* defaults - an optional dict of key=val parameters
* params - pass arguments as either key=val pairs, or as
key=None if key is a command line switch
"""
cmd = sequtil.find_exec(hmmcmd)
if cmd is None:
raise OSError("%s could not be found" % hmmcmd)
os_type = sequtil.get_os_type()
log.debug("os type is set as %s" % os_type)
infile = os.path.abspath(infile)
if outfile:
outfile = os.path.abspath(outfile)
elif outfile is None:
outfile = os.path.join(os.path.split(infile)[0], sequtil.randomname(length=10))
outin = [infile]
if not outfile is False:
outin.insert(0, outfile)
if defaults is None:
defaults = {}
defaults.update(params)
args = [cmd]
for k, v in defaults.items():
if len(k) == 1:
dashes = "-"
else:
dashes = "--"
if v is None:
fstr = "%(dashes)s%(k)s"
elif len(str(v).split()) > 1:
fstr = '%(dashes)s%(k)s "%(v)s"'
else:
fstr = "%(dashes)s%(k)s %(v)s"
args.append(fstr % locals())
args.extend(outin)
log.info(" ".join(args))
if os_type == "POSIX" and not dryrun:
# subprocess.check_call(args)
if quiet:
stdout = open(os.devnull)
else:
stdout = None
subprocess.Popen(args, stdout=stdout).communicate()
elif os_type == "WINDOWS":
# completely untested
cwd, _ = os.path.split(target_file)
cmds = ['cd "%s"' % cwd, cmd]
sequtil.run_bat(cmds, path=cwd, run=not dryrun)
return outfile
