Exemple #1
0
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)
Exemple #2
0
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)
Exemple #3
0
    #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
)
Exemple #5
0
                    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(",")