print "# testing: IsSingleFastaDna(fname)"
print " %s" % IsSingleFastaDna(fname)
print "# testing: IsSingleFastaProtein(fname)"
print " %s" % IsSingleFastaProtein(fname)
print "# testing: parseFasta(content,allow_decorated_headers=True)"
_seqs = parseFasta(open(fname),allow_decorated_headers=True)
print " %s..." % str(tuple(_seqs.keys()[0:5]))
print "# testing: parseFasta(content,allow_decorated_headers=False)"
_seqs = parseFasta(open(fname),allow_decorated_headers=False)
print " %s..." % str(tuple(_seqs.keys()[0:5]))
print "# testing: parseDecoratedFasta(content)"
_seqs,_info = parseDecoratedFasta(open(fname))
print " %s..." % str(tuple(_seqs.keys()[0:5]))
print " %s..." % str(dict([(h,k) for h,k in _info.items()[0:5] ]))
# end of function __test
if __name__ == "__main__":
import sys
from os.path import isfile as osPathIsfile
print """ Functions for parsing,accessing and writing FASTA files """
print """ Unit testing: [ %s test ] [ %s test SINGLE_FASTA_FNAME ] """ % (sys.argv[0],sys.argv[0])
if not 'test' in sys.argv: sys.exit()
fname = None
if len(sys.argv) == 3:
fname = sys.argv[2]
if not osPathIsfile(fname):
fname = None
# test all the functions
__test(fname=fname)
def runcexpander(fname_fasta, cbalignp_commandline=" -y", output='binary'):
"""
Run the complete cascade of cexpander algorithms on an input multi fasta
file and return the output as a CexpanderOutput object
@type fname_fasta: string
@param fname_fasta: path to input multi fasta file
@type cbalignp_commandline: string
@param cbalignp_commandline: (extra) command line for cbalignp
@type min_cols: integer
@param min_cols: minimal number of uniformly matched positions (cols)
required to report transfer blocks for (>= 0)
@type projected_on: string
@param projected_on: apply fasta seqeunce header which to use for projection;
apply ':::' to do projections on all input sequences
@attention: requires global variable EXECUTABLE_cexpander_ALLVSALL
@attention: requires global variable EXECUTABLE_CEXPANDER_CBALIGNP
@attention: requires global variable EXECUTABLE_CEXPANDER_CEXPANDER
@attention: see cexpander_dr for (additional) command line options
@attention: only a subset of cexpander_dr commandline options are supported!
@rtype: CexpanderOutput object
@return: CexpanderOutput object
"""
if not fname_fasta: raise "NoProperFunctionArguments"
if not osPathIsfile(fname_fasta): raise "FileDoesNotExist"
# (0) create (~unique) filenames
uniquetag = get_random_string_tag()
fname_allvsall = ".".join([fname_fasta, uniquetag, "allvsall"])
fname_report = ".".join([fname_fasta, uniquetag, "report"])
fname_aligned = ".".join([fname_fasta, uniquetag, "aligned"])
fname_settings = ".".join([fname_fasta, uniquetag, "settings"])
fname_cexpander = ".".join([fname_fasta, uniquetag, "cexpander"])
# (1) create complete .fa -> cexpanderstring command
command = """
python %s %s %s %s;
%s -i %s %s > %s;
%s < %s;
""" % (
EXECUTABLE_CEXPANDER_ALLVSALL,
fname_fasta,
fname_allvsall,
fname_report,
EXECUTABLE_CEXPANDER_CBALIGNP,
fname_allvsall,
cbalignp_commandline,
fname_aligned,
EXECUTABLE_CEXPANDER_CEXPANDER,
fname_settings,
)
# (2) create fname_settings file
binorfloat = "$dumpcv"
if output == "float": binorfloat = "$dumpcvc"
fh = open(fname_settings, 'w')
content = "\n\n".join([
"$load\n%s\n%s" % (fname_report, fname_aligned),
"$addquery\n-1",
"$run",
"$dumpentries",
"$cv_linear",
"%s" % (binorfloat), # BINARY == $dumpcv, FLOAT = $dumpcvc
"$exit\n\n",
])
fh.write(content)
fh.close()
# (3) run the command
ci, co, ce = osPopen3(command)
ci.close()
# output of EXECUTABLE_CEXPANDER_ALLVSALL is cast to STDOUT as well!
cexpanderdata = co.read()
co.close()
error = ce.read()
ce.close()
# (4) parse fname_cexpander to CexpanderOutput object
cxpdr = parse_cexpander(cexpanderdata, fname_fasta)
# (5) cleanup files
osSystem("rm -f %s %s.%s.*" % (fname_fasta, fname_fasta, uniquetag))
# (6) return the output object
return cxpdr
def runcexpander(fname_fasta,cbalignp_commandline=" -y",output='binary'):
"""
Run the complete cascade of cexpander algorithms on an input multi fasta
file and return the output as a CexpanderOutput object
@type fname_fasta: string
@param fname_fasta: path to input multi fasta file
@type cbalignp_commandline: string
@param cbalignp_commandline: (extra) command line for cbalignp
@type min_cols: integer
@param min_cols: minimal number of uniformly matched positions (cols)
required to report transfer blocks for (>= 0)
@type projected_on: string
@param projected_on: apply fasta seqeunce header which to use for projection;
apply ':::' to do projections on all input sequences
@attention: requires global variable EXECUTABLE_cexpander_ALLVSALL
@attention: requires global variable EXECUTABLE_CEXPANDER_CBALIGNP
@attention: requires global variable EXECUTABLE_CEXPANDER_CEXPANDER
@attention: see cexpander_dr for (additional) command line options
@attention: only a subset of cexpander_dr commandline options are supported!
@rtype: CexpanderOutput object
@return: CexpanderOutput object
"""
if not fname_fasta: raise "NoProperFunctionArguments"
if not osPathIsfile(fname_fasta): raise "FileDoesNotExist"
# (0) create (~unique) filenames
uniquetag = get_random_string_tag()
fname_allvsall = ".".join([fname_fasta,uniquetag,"allvsall"])
fname_report = ".".join([fname_fasta,uniquetag,"report"])
fname_aligned = ".".join([fname_fasta,uniquetag,"aligned"])
fname_settings = ".".join([fname_fasta,uniquetag,"settings"])
fname_cexpander = ".".join([fname_fasta,uniquetag,"cexpander"])
# (1) create complete .fa -> cexpanderstring command
command = """
python %s %s %s %s;
%s -i %s %s > %s;
%s < %s;
""" % (
EXECUTABLE_CEXPANDER_ALLVSALL,
fname_fasta,
fname_allvsall,
fname_report,
EXECUTABLE_CEXPANDER_CBALIGNP,
fname_allvsall,
cbalignp_commandline,
fname_aligned,
EXECUTABLE_CEXPANDER_CEXPANDER,
fname_settings,
)
# (2) create fname_settings file
binorfloat = "$dumpcv"
if output == "float": binorfloat = "$dumpcvc"
fh = open(fname_settings,'w')
content = "\n\n".join( [
"$load\n%s\n%s" % (fname_report,fname_aligned),
"$addquery\n-1",
"$run",
"$dumpentries",
"$cv_linear",
"%s" % ( binorfloat ), # BINARY == $dumpcv, FLOAT = $dumpcvc
"$exit\n\n",
] )
fh.write(content)
fh.close()
# (3) run the command
ci,co,ce = osPopen3(command)
ci.close()
# output of EXECUTABLE_CEXPANDER_ALLVSALL is cast to STDOUT as well!
cexpanderdata = co.read()
co.close()
error = ce.read()
ce.close()
# (4) parse fname_cexpander to CexpanderOutput object
cxpdr = parse_cexpander(cexpanderdata,fname_fasta)
# (5) cleanup files
osSystem("rm -f %s %s.%s.*" % ( fname_fasta, fname_fasta,uniquetag ) )
# (6) return the output object
return cxpdr