def cmalign(cmfile, fastafile, outfile=None, statsfile=None,
defaults=None, quiet=False, dryrun=False, **params):
"""
Align sequences in fastafile against profile defined in cmfile.
required arguments
------------------
* cmfile - alignment profile, eg, output of cmbuild
* fastafile - file containing sequences in fasta format
optional arguments
------------------
* outfile - name of output alignment (Stockholm format); uses
name of fasta file if None
* statsfile - optional filename for alignment statistics
* defaults, quiet, dryrun, params - see help(Seq.run_infernal._run)
output
------
returns a two-tuple: (outfile, align_data)
* outfile - name of output file containing the alignment
* align_data - output of Seq.run_infernal.parse_cmstats
"""
cmfile = os.path.abspath(cmfile)
fastafile = os.path.abspath(fastafile)
if outfile:
outfile = os.path.abspath(outfile)
elif outfile is None:
outfile = os.path.join(os.path.split(fastafile)[0], sequtil.randomname(length=10)+'.sto')
stdoutdata, stderrdata = _run('cmalign',
o=outfile,
args=[cmfile, fastafile],
quiet=quiet,
dryrun=dryrun,
**params)
if not stderrdata and not dryrun:
if not statsfile:
statsfile = os.path.splitext(outfile)[0]+'.cmalign'
open(statsfile,'w').write(stdoutdata)
align_data = parse_cmstats(stdoutdata)
else:
outfile, align_data = None, None
return outfile, align_data
def cmbuild(infile, outfile=None, defaults=None, quiet=False, dryrun=False, **params):
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)+'.cm')
stdoutdata, stderrdata = _run('cmbuild',
F=None,
args=[outfile, infile],
quiet=quiet,
dryrun=dryrun,
**params)
return outfile
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