def main():
# parse some argument lists
inputArgs = parser.parse_args()
#### PathoID modules ####
start = time();
if (inputArgs.subcommand=='LIB'):
################################################$
#append taxon id in the front of sequence header
################################################$
NAs = 'X'
if inputArgs.lib_dbuser!=NAs and inputArgs.lib_dbpasswd==NAs:
print 'if you want to use mysql, make sure that you install pathoDB and '
'also specify the corresponding mysql password correctly '
'(Ask your mysql admin to access the database).'
MysqlConf=(inputArgs.lib_dbhost,inputArgs.lib_dbport,inputArgs.lib_dbuser,inputArgs.lib_dbpasswd,inputArgs.lib_db)
taxon_ids=pathoLib.parse_input_app_build_nt_tgt(inputArgs.lib_taxon_ids)
exclude_taxon_ids=pathoLib.parse_input_app_build_nt_tgt(inputArgs.lib_exclude_taxon_ids)
(ncbiNt_ti,ncbiNt_invalid) = pathoLib.append_ti_into_fasta_app(inputArgs.lib_reference,
taxon_ids, exclude_taxon_ids, inputArgs.lib_subtax,MysqlConf,
not(inputArgs.lib_nodesc), inputArgs.lib_online_search, inputArgs.lib_outprefix,
inputArgs.lib_outdir)
if (inputArgs.subcommand=='MAP'):
pathoMapOptions = PathoMapA.PathoMapOptions()
pathoMapOptions.verbose = inputArgs.verbose
pathoMapOptions.outDir = inputArgs.map_outdir
pathoMapOptions.indexDir = inputArgs.map_indexdir
pathoMapOptions.outAlignFile = inputArgs.map_outalign
pathoMapOptions.inReadFile = inputArgs.map_inputread
pathoMapOptions.inReadFilePair1 = inputArgs.map_inputread1
pathoMapOptions.inReadFilePair2 = inputArgs.map_inputread2
pathoMapOptions.targetAlignParameters = inputArgs.map_targetalignparams
pathoMapOptions.filterAlignParameters = inputArgs.map_filteralignparams
if (len(inputArgs.map_targetref)>0):
pathoMapOptions.targetRefFiles = inputArgs.map_targetref.split(",")
if (len(inputArgs.map_filterref)>0):
pathoMapOptions.filterRefFiles = inputArgs.map_filterref.split(",")
if (len(inputArgs.map_targetindex)>0):
pathoMapOptions.targetIndexPrefixes = inputArgs.map_targetindex.split(",")
if (len(inputArgs.map_filterindex)>0):
pathoMapOptions.filterIndexPrefixes = inputArgs.map_filterindex.split(",")
if (len(inputArgs.map_targetalign)>0):
pathoMapOptions.targetAlignFiles = inputArgs.map_targetalign.split(",")
if (len(inputArgs.map_filteralign)>0):
pathoMapOptions.filterAlignFiles = inputArgs.map_filteralign.split(",")
pathoMapOptions.btHome = inputArgs.map_bthome
pathoMapOptions.numThreads = inputArgs.map_numthreads
pathoMapOptions.exp_tag = inputArgs.map_exp_tag + "-"
PathoMapA.processPathoMap(pathoMapOptions)
if (inputArgs.subcommand=='ID'):
pathoIdOptions = PathoID.PathoIdOptions(inputArgs.id_ali_file)
pathoIdOptions.ali_format = inputArgs.id_ali_format
pathoIdOptions.verbose = inputArgs.verbose
pathoIdOptions.out_matrix_flag = inputArgs.id_out_matrix
pathoIdOptions.score_cutoff = inputArgs.id_score_cutoff
pathoIdOptions.exp_tag = inputArgs.id_exp_tag
pathoIdOptions.outdir = inputArgs.id_outdir
pathoIdOptions.emEpsilon = inputArgs.id_emEpsilon
pathoIdOptions.maxIter = inputArgs.id_maxIter
pathoIdOptions.piPrior = inputArgs.id_piPrior
pathoIdOptions.thetaPrior = inputArgs.id_thetaPrior
pathoIdOptions.noalign = inputArgs.id_noalign
pathoIdOptions.noCutOff = inputArgs.id_nocutoff
PathoID.pathoscope_reassign(pathoIdOptions)
if (inputArgs.subcommand=='REP'):
pathoReportOptions = PathoReportA.PathoReportOptions(inputArgs.rep_ali_file)
pathoReportOptions.verbose = inputArgs.verbose
pathoReportOptions.contigFlag = inputArgs.rep_contig_flag
pathoReportOptions.outDir = inputArgs.rep_outdir
pathoReportOptions.samtoolsHome = inputArgs.rep_samtoolshome
pathoReportOptions.noCutOff = inputArgs.rep_nocutoff
mysqlConf=(inputArgs.rep_dbhost,inputArgs.rep_dbport,inputArgs.rep_dbuser,
inputArgs.rep_dbpasswd,inputArgs.rep_db)
pathoReportOptions.mysqlConf = mysqlConf
PathoReportA.processPathoReport(pathoReportOptions)
if (inputArgs.subcommand=='QC'):
qcargs = sys.argv[2:]
pathoqcdir = pathoscopedir + os.path.sep + 'pathoscope' + os.path.sep + 'pathoqc'
pathoqcfile = pathoqcdir + os.path.sep + 'pathoqc.py'
if os.path.exists(pathoqcfile):
cmd = sys.executable
cmd += " " + pathoqcfile + " "
cmd += " ".join(qcargs)
print(cmd)
os.system(cmd)
else:
print("PathoQC (" + pathoqcfile + ") not found. Please download pathoqc_vXXX.tar.gz and "
"install it ("+pathoqcdir+") from http://sourceforge.net/projects/pathoscope/")
elapsed = time() - start;
if inputArgs.verbose:
print "Total Elapsed Time: %d" % (elapsed)
def main():
# parse some argument lists
inputArgs = parser.parse_args()
#### PathoID modules ####
start = time()
if (inputArgs.subcommand == 'LIB'):
################################################$
#append taxon id in the front of sequence header
################################################$
NAs = 'X'
if inputArgs.lib_dbuser != NAs and inputArgs.lib_dbpasswd == NAs:
print 'if you want to use mysql, make sure that you install pathoDB and '
'also specify the corresponding mysql password correctly '
'(Ask your mysql admin to access the database).'
MysqlConf = (inputArgs.lib_dbhost, inputArgs.lib_dbport,
inputArgs.lib_dbuser, inputArgs.lib_dbpasswd,
inputArgs.lib_db)
taxon_ids = pathoLib.parse_input_app_build_nt_tgt(
inputArgs.lib_taxon_ids)
exclude_taxon_ids = pathoLib.parse_input_app_build_nt_tgt(
inputArgs.lib_exclude_taxon_ids)
(ncbiNt_ti, ncbiNt_invalid) = pathoLib.append_ti_into_fasta_app(
inputArgs.lib_reference, taxon_ids, exclude_taxon_ids,
inputArgs.lib_subtax, MysqlConf, not (inputArgs.lib_nodesc),
inputArgs.lib_online_search, inputArgs.lib_outprefix,
inputArgs.lib_outdir)
if (inputArgs.subcommand == 'MAP'):
pathoMapOptions = PathoMapA.PathoMapOptions()
pathoMapOptions.verbose = inputArgs.verbose
pathoMapOptions.outDir = inputArgs.map_outdir
pathoMapOptions.indexDir = inputArgs.map_indexdir
pathoMapOptions.outAlignFile = inputArgs.map_outalign
pathoMapOptions.inReadFile = inputArgs.map_inputread
pathoMapOptions.inReadFilePair1 = inputArgs.map_inputread1
pathoMapOptions.inReadFilePair2 = inputArgs.map_inputread2
pathoMapOptions.targetAlignParameters = inputArgs.map_targetalignparams
pathoMapOptions.filterAlignParameters = inputArgs.map_filteralignparams
if (len(inputArgs.map_targetref) > 0):
pathoMapOptions.targetRefFiles = inputArgs.map_targetref.split(",")
if (len(inputArgs.map_filterref) > 0):
pathoMapOptions.filterRefFiles = inputArgs.map_filterref.split(",")
if (len(inputArgs.map_targetindex) > 0):
pathoMapOptions.targetIndexPrefixes = inputArgs.map_targetindex.split(
",")
if (len(inputArgs.map_filterindex) > 0):
pathoMapOptions.filterIndexPrefixes = inputArgs.map_filterindex.split(
",")
if (len(inputArgs.map_targetalign) > 0):
pathoMapOptions.targetAlignFiles = inputArgs.map_targetalign.split(
",")
if (len(inputArgs.map_filteralign) > 0):
pathoMapOptions.filterAlignFiles = inputArgs.map_filteralign.split(
",")
pathoMapOptions.btHome = inputArgs.map_bthome
pathoMapOptions.numThreads = inputArgs.map_numthreads
pathoMapOptions.exp_tag = inputArgs.map_exp_tag + "-"
PathoMapA.processPathoMap(pathoMapOptions)
if (inputArgs.subcommand == 'ID'):
pathoIdOptions = PathoID.PathoIdOptions(inputArgs.id_ali_file)
pathoIdOptions.ali_format = inputArgs.id_ali_format
pathoIdOptions.verbose = inputArgs.verbose
pathoIdOptions.out_matrix_flag = inputArgs.id_out_matrix
pathoIdOptions.score_cutoff = inputArgs.id_score_cutoff
pathoIdOptions.exp_tag = inputArgs.id_exp_tag
pathoIdOptions.outdir = inputArgs.id_outdir
pathoIdOptions.emEpsilon = inputArgs.id_emEpsilon
pathoIdOptions.maxIter = inputArgs.id_maxIter
pathoIdOptions.piPrior = inputArgs.id_piPrior
pathoIdOptions.thetaPrior = inputArgs.id_thetaPrior
pathoIdOptions.noalign = inputArgs.id_noalign
pathoIdOptions.noCutOff = inputArgs.id_nocutoff
PathoID.pathoscope_reassign(pathoIdOptions)
if (inputArgs.subcommand == 'REP'):
pathoReportOptions = PathoReportA.PathoReportOptions(
inputArgs.rep_ali_file)
pathoReportOptions.verbose = inputArgs.verbose
pathoReportOptions.contigFlag = inputArgs.rep_contig_flag
pathoReportOptions.outDir = inputArgs.rep_outdir
pathoReportOptions.samtoolsHome = inputArgs.rep_samtoolshome
pathoReportOptions.noCutOff = inputArgs.rep_nocutoff
mysqlConf = (inputArgs.rep_dbhost, inputArgs.rep_dbport,
inputArgs.rep_dbuser, inputArgs.rep_dbpasswd,
inputArgs.rep_db)
pathoReportOptions.mysqlConf = mysqlConf
PathoReportA.processPathoReport(pathoReportOptions)
if (inputArgs.subcommand == 'QC'):
qcargs = sys.argv[2:]
pathoqcdir = pathoscopedir + os.path.sep + 'pathoscope' + os.path.sep + 'pathoqc'
pathoqcfile = pathoqcdir + os.path.sep + 'pathoqc.py'
if os.path.exists(pathoqcfile):
cmd = sys.executable
cmd += " " + pathoqcfile + " "
cmd += " ".join(qcargs)
print(cmd)
os.system(cmd)
else:
print(
"PathoQC (" + pathoqcfile +
") not found. Please download pathoqc_vXXX.tar.gz and "
"install it (" + pathoqcdir +
") from http://sourceforge.net/projects/pathoscope/")
elapsed = time() - start
if inputArgs.verbose:
print "Total Elapsed Time: %d" % (elapsed)
#append taxon id in the front of sequence header
################################################$
NAs = 'X'
if inputArgs.lib_dbuser != NAs and inputArgs.lib_dbpasswd == NAs:
print 'if you want to use mysql, make sure that you install pathoDB and '
'also specify the corresponding mysql password correctly '
'(Ask your mysql admin to access the database).'
MysqlConf = (inputArgs.lib_dbhost, inputArgs.lib_dbport,
inputArgs.lib_dbuser, inputArgs.lib_dbpasswd,
inputArgs.lib_db)
taxon_ids = pathoLib.parse_input_app_build_nt_tgt(inputArgs.lib_taxon_ids)
exclude_taxon_ids = pathoLib.parse_input_app_build_nt_tgt(
inputArgs.lib_exclude_taxon_ids)
(ncbiNt_ti, ncbiNt_invalid) = pathoLib.append_ti_into_fasta_app(
inputArgs.lib_reference, taxon_ids, exclude_taxon_ids,
inputArgs.lib_subtax, MysqlConf, not (inputArgs.lib_nodesc),
inputArgs.lib_online_search, inputArgs.lib_outprefix,
inputArgs.lib_outdir)
if (inputArgs.subcommand == 'MAP'):
pathoMapOptions = PathoMapA.PathoMapOptions()
pathoMapOptions.verbose = inputArgs.verbose
pathoMapOptions.outDir = inputArgs.map_outdir
pathoMapOptions.indexDir = inputArgs.map_indexdir
pathoMapOptions.outAlignFile = inputArgs.map_outalign
pathoMapOptions.inReadFile = inputArgs.map_inputread
pathoMapOptions.inReadFilePair1 = inputArgs.map_inputread1
pathoMapOptions.inReadFilePair2 = inputArgs.map_inputread2
pathoMapOptions.targetAlignParameters = inputArgs.map_targetalignparams
pathoMapOptions.filterAlignParameters = inputArgs.map_filteralignparams
if (len(inputArgs.map_targetref) > 0):
"-p",
action="store",
dest="passwd",
required=False,
default="johnsonlab",
help="provide password associate with user",
)
parser.add_argument(
"-o",
action="store",
dest="label",
required=True,
help="provide a short description (w/o any white space) of the target database you are about to build",
)
parser.add_argument("--version", action="version", version="%(prog)s 1.0")
args = parser.parse_args()
################################################$
# append taxon id in the front of sequence header
################################################$
NAs = "X"
if args.user != NAs and args.user == NAs:
print "if you want to use mysql, make sure that you install pathoDB and also specify the corresponding mysql password correclty(Ask to your mysql admin to access the database)."
MysqlConf = (args.hostname, args.myport, args.user, args.passwd, "information_schema")
taxon_ids = pathoLib.parse_input_app_build_nt_tgt(args.taxon_ids)
(ncbiNt_ti, ncbiNt_invalid) = pathoLib.append_ti_into_fasta_app(
args.reference, taxon_ids, args.subtax, MysqlConf, args.desc, args.online_search, args.label
)
action='store',
dest='passwd',
required=False,
default='johnsonlab',
help='provide password associate with user')
parser.add_argument(
'-o',
action='store',
dest='label',
required=True,
help=
'provide a short description (w/o any white space) of the target database you are about to build'
)
parser.add_argument('--version', action='version', version='%(prog)s 1.0')
args = parser.parse_args()
################################################$
#append taxon id in the front of sequence header
################################################$
NAs = 'X'
if args.user != NAs and args.user == NAs:
print 'if you want to use mysql, make sure that you install pathoDB and also specify the corresponding mysql password correclty(Ask to your mysql admin to access the database).'
MysqlConf = (args.hostname, args.myport, args.user, args.passwd,
'information_schema')
taxon_ids = pathoLib.parse_input_app_build_nt_tgt(args.taxon_ids)
(ncbiNt_ti, ncbiNt_invalid) = pathoLib.append_ti_into_fasta_app(
args.reference, taxon_ids, args.subtax, MysqlConf, args.desc,
args.online_search, args.label)
start = time();
if (inputArgs.subcommand=='LIB'):
################################################$
#append taxon id in the front of sequence header
################################################$
NAs = 'X'
if inputArgs.lib_dbuser!=NAs and inputArgs.lib_dbpasswd==NAs:
print 'if you want to use mysql, make sure that you install pathoDB and '
'also specify the corresponding mysql password correctly '
'(Ask your mysql admin to access the database).'
MysqlConf=(inputArgs.lib_dbhost,inputArgs.lib_dbport,inputArgs.lib_dbuser,inputArgs.lib_dbpasswd,inputArgs.lib_db)
taxon_ids=pathoLib.parse_input_app_build_nt_tgt(inputArgs.lib_taxon_ids)
exclude_taxon_ids=pathoLib.parse_input_app_build_nt_tgt(inputArgs.lib_exclude_taxon_ids)
(ncbiNt_ti,ncbiNt_invalid) = pathoLib.append_ti_into_fasta_app(inputArgs.lib_reference,
taxon_ids, exclude_taxon_ids, inputArgs.lib_subtax,MysqlConf,
not(inputArgs.lib_nodesc), inputArgs.lib_online_search, inputArgs.lib_outprefix,
inputArgs.lib_outdir)
if (inputArgs.subcommand=='MAP'):
pathoMapOptions = PathoMapA.PathoMapOptions()
pathoMapOptions.verbose = inputArgs.verbose
pathoMapOptions.outDir = inputArgs.map_outdir
pathoMapOptions.indexDir = inputArgs.map_indexdir
pathoMapOptions.outAlignFile = inputArgs.map_outalign
pathoMapOptions.inReadFile = inputArgs.map_inputread
pathoMapOptions.inReadFilePair1 = inputArgs.map_inputread1
pathoMapOptions.inReadFilePair2 = inputArgs.map_inputread2
pathoMapOptions.targetAlignParameters = inputArgs.map_targetalignparams
pathoMapOptions.filterAlignParameters = inputArgs.map_filteralignparams
if (len(inputArgs.map_targetref)>0):
pathoMapOptions.targetRefFiles = inputArgs.map_targetref.split(",")