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)
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
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
mysqlConf = (inputArgs.rep_dbhost, inputArgs.rep_dbport,
inputArgs.rep_dbuser, inputArgs.rep_dbpasswd,
inputArgs.rep_db)
pathoReportOptions.mysqlConf = mysqlConf
PathoReportA.processPathoReport(pathoReportOptions)
elapsed = time() - start
default='testset',
dest='exp_tag',
help='Experiment tag')
parser.add_argument('-outdir',
action='store',
default='.',
dest='outdir',
help='Output Directory')
parser.add_argument('--version', action='version', version='%(prog)s 1.0')
parser.add_argument('-t',
action='store',
default='sam',
dest='ali_format',
help='Alignment Format: sam/bl8/gnu-sam')
parser.add_argument('-f',
action='store',
dest='ali_file',
required=True,
help='Alignment file path')
inputArgs = parser.parse_args()
start = time()
PathoID.pathoscope_reassign(inputArgs.out_matrix, inputArgs.verbose,
inputArgs.score_cutoff, inputArgs.exp_tag,
inputArgs.ali_format, inputArgs.ali_file,
inputArgs.outdir, inputArgs.emEpsilon,
inputArgs.maxIter, not (inputArgs.noalign))
elapsed = time() - start
if inputArgs.verbose:
print "EM Elapsed Time: %d" % (elapsed)
parser.add_argument('-o', action='store_true', default=False, dest='out_matrix',
help='Output alignment matrix')
parser.add_argument('-noUpdatedAlignFile', action='store_true', default=False, dest='noalign',
help='Do not generate an updated alignment file')
parser.add_argument('-verbose', action='store_true', default=False, dest='verbose',
help='Prints verbose text while running')
parser.add_argument('-s', action='store', default=0.01, type=float,
dest='score_cutoff', help='Score Cutoff')
parser.add_argument('-emEpsilon', action='store', default=1e-7, type=float,
dest='emEpsilon', help='EM Algorithm Epsilon cutoff')
parser.add_argument('-maxIter', action='store', default=50, type=int,
dest='maxIter', help='EM Algorithm maximum iterations')
parser.add_argument('-e', action='store', default='testset', dest='exp_tag',
help='Experiment tag')
parser.add_argument('-outdir', action='store', default='.', dest='outdir',
help='Output Directory')
parser.add_argument('--version', action='version', version=VERSION)
parser.add_argument('-t', action='store', default='sam', dest='ali_format',
help='Alignment Format: sam/bl8/gnu-sam')
parser.add_argument('-f', action='store', dest='ali_file', required=True,
help='Alignment file path')
inputArgs = parser.parse_args()
start = time();
PathoID.pathoscope_reassign(inputArgs.out_matrix, inputArgs.verbose,
inputArgs.score_cutoff, inputArgs.exp_tag, inputArgs.ali_format, inputArgs.ali_file,
inputArgs.outdir, inputArgs.emEpsilon, inputArgs.maxIter, not(inputArgs.noalign))
elapsed = time() - start;
if inputArgs.verbose:
print "EM Elapsed Time: %d" % (elapsed)
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 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 mysqlConf=(inputArgs.rep_dbhost,inputArgs.rep_dbport,inputArgs.rep_dbuser, inputArgs.rep_dbpasswd,inputArgs.rep_db) pathoReportOptions.mysqlConf = mysqlConf PathoReportA.processPathoReport(pathoReportOptions) elapsed = time() - start; if inputArgs.verbose: print "Total Elapsed Time: %d" % (elapsed)