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Best Python code snippet using localstack_python
rmvRedundancy.py
Source:rmvRedundancy.py 
1#!/usr/bin/env python2"""3This program removes redundancy among queries compared to subjects.4"""5import os6import sys7import getopt8import logging9import time10import shutil11from pyRepet.launcher.programLauncher import programLauncher12from pyRepetUnit.commons.launcher.Launcher import Launcher13from pyRepetUnit.commons.sql.RepetJob import RepetJob14from pyRepetUnit.commons.seq.FastaUtils import FastaUtils15import ConfigParser16def help():17 """18 Give the list of the command-line options.19 """20 print21 print "usage:",sys.argv[0]," [ options ]"22 print "options:"23 print " -h: this help"24 print " -q: fasta filename of the queries"25 print " -s: fasta filename of the subjects (same as queries if not specified)"26 print " -o: output queries fasta filename (default=qryFileName+'.uniq')"27 print " -i: identity threshold (default=0.95)"28 print " -l: length threshold (default=0.98)"29 print " -e: E-value threshold (default=1e-10)"30 print " -f: length filter for Blaster (default=100)"31 print " -Q: queue name to run in parallel"32 print " -C: name of the configuration file"33 print " -n: max. number of jobs (default=100,given a min. of 1 query per job)"34 print " -c: clean"35 print " -v: verbose (default=0/1/2)"36 print37def main():38 """39 This program removes redundancy among queries compared to subjects.40 """41 qryFileName = ""42 sbjFileName = ""43 outFileName = ""44 thresIdentity = 0.95 # remove the seq if it is identical to 95% of another seq45 thresLength = 0.98 # and if its length is 98% of that seq46 threshEvalue = "1e-10"47 lengthFilter = 10048 useCluster = False49 queue = ""50 configFileName = ""51 maxNbJobs = 10052 clean = False53 verbose = 054 try:55 opts, args = getopt.getopt(sys.argv[1:],"hq:s:o:L:i:l:e:w:f:Q:C:n:cv:")56 except getopt.GetoptError, err:57 print str(err)58 help()59 sys.exit(1)60 for o,a in opts:61 if o == "-h":62 help()63 sys.exit(0)64 elif o == "-q":65 qryFileName = a 66 elif o == "-s":67 sbjFileName = a 68 elif o == "-o":69 outFileName = a70 elif o == "-i":71 thresIdentity = float(a) 72 elif o == "-l":73 thresLength = float(a)74 elif o == "-e":75 threshEvalue = a76 elif o == "-f":77 lengthFilter = int(a)78 elif o == "-Q":79 useCluster = True80 queue = a81 elif o == "-C":82 configFileName = a83 elif o == "-n":84 maxNbJobs = int(a)85 elif o == "-c":86 clean = True87 elif o == "-v":88 verbose = int(a)89 90 if thresIdentity > 1.0 or thresLength > 1.0:91 print "ERROR: thresholds must be <= 1.0"92 sys.exit(1)93 if qryFileName == "":94 print "ERROR: missing input file (-q)"95 help()96 sys.exit(1)97 if configFileName == "":98 print "ERROR: missing configuration file (-C)"99 sys.exit(1)100 if not os.path.exists( configFileName ):101 print "ERROR: configuration file doesn't exist"102 sys.exit(1)103 #--------------------------------------------------------------------------104 if verbose > 0:105 print "START %s (%s)" % ( sys.argv[0].split("/")[-1],106 time.strftime("%m/%d/%Y %H:%M:%S") )107 sys.stdout.flush()108 if outFileName == "":109 outFileName = "%s.uniq" % ( qryFileName )110 111 uniqId = "%s-%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )112 # create the 'log' file113 logFileName = "%s_rmvRedundancy_%s.log" % ( outFileName, uniqId )114 handler = logging.FileHandler( logFileName )115 formatter = logging.Formatter( "%(asctime)s %(levelname)s: %(message)s" )116 handler.setFormatter( formatter )117 logging.getLogger('').addHandler( handler )118 logging.getLogger('').setLevel( logging.DEBUG )119 logging.info( "started" )120 if not os.path.exists( qryFileName ):121 string = "query file '%s' doesn't exist" % ( qryFileName )122 logging.error( string )123 print "ERROR: %s" % ( string )124 sys.exit(1)125 if sbjFileName != "":126 if not os.path.exists( sbjFileName ):127 string = "subject file '%s' doesn't exist" % ( sbjFileName )128 logging.error( string )129 print "ERROR: %s" % ( string )130 sys.exit(1)131 else:132 sbjFileName = qryFileName133 logging.info( "remove redundancy among '%s' (queries) compare to '%s' (subjects)" % ( qryFileName, sbjFileName ) )134 #--------------------------------------------------------------------------135 # check the input files are not empty, otherwise exit136 nbSeqQry = FastaUtils.dbSize( qryFileName )137 if nbSeqQry == 0:138 string = "query file is empty"139 logging.info( string )140 print "WARNING: %s" % ( string )141 logging.info( "finished" )142 sys.exit(0)143 nbSeqSbj = FastaUtils.dbSize( sbjFileName )144 if sbjFileName != qryFileName:145 nbSeqSbj = FastaUtils.dbSize( sbjFileName )146 if nbSeqSbj == 0:147 string = "subject file is empty"148 logging.info( string )149 print "WARNING: %s" % ( string )150 logging.info( "finished" )151 sys.exit(0)152 #--------------------------------------------------------------------------153 pL = programLauncher()154 uniqTmpDir = "tmp%s" % ( uniqId )155 if os.path.exists( uniqTmpDir ):156 shutil.rmtree( uniqTmpDir )157 os.mkdir( uniqTmpDir )158 os.chdir( uniqTmpDir )159 os.system( "ln -s ../%s ." % ( qryFileName ) )160 if sbjFileName != qryFileName:161 os.system( "ln -s ../%s ." % ( sbjFileName ) )162 os.system( "ln -s ../%s ." % ( logFileName ) )163 if useCluster:164 os.system( "ln -s ../%s ." % ( configFileName ) )165 config = ConfigParser.ConfigParser()166 config.readfp( open(configFileName) )167 queue = config.get("classif_consensus", "resources")168 cDir = os.getcwd()169 if config.get("classif_consensus", "tmpDir" ) != "":170 tmpDir = config.get("classif_consensus", "tmpDir")171 else:172 tmpDir = cDir173 lCmds=[]174 # shorten sequence headers175 if sbjFileName == qryFileName:176 # sort sequences by increasing length177 178 os.system( "mv %s %s.initOrder" % ( qryFileName, qryFileName ) )179 180 prg = os.environ["REPET_PATH"] + "/bin/srptSortSequencesByIncreasingLength.py"181 cmd = prg182 cmd += " -i %s.initOrder" % ( qryFileName )183 cmd += " -o %s" % ( qryFileName )184 cmd += " -v %d" % ( verbose-1 )185 lCmds.append(cmd)186 prg = os.environ["REPET_PATH"] + "/bin/shortenSeqHeader.py"187 cmd = prg188 cmd += " -i %s" % ( qryFileName )189 lCmds.append(cmd)190 if not useCluster:191 for c in lCmds:192 pL.launch( prg, c )193 else:194 groupid = "%s_SubjectEqualQuery_sortSequencesAndShortenSeqHeader" % ( "rmvRedundancy" )195 acronym = "sortSequencesAndShortenSeqHeader"196 jobdb = RepetJob( cfgFileName = configFileName )197 cLauncher = Launcher( jobdb, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid, acronym )198 cLauncher.beginRun()199 cLauncher.job.jobname = acronym200 cmd_start = ""201 cmd_start += "os.system( \"ln -s %s/%s.initOrder .\" )\n" % ( cDir, qryFileName )202 for c in lCmds:203 cmd_start += "log = os.system( \""204 cmd_start += c205 cmd_start += "\" )\n"206 cmd_finish = "if not os.path.exists( \"%s/%s.shortH\" ):\n" % ( cDir, qryFileName )207 cmd_finish += "\tos.system( \"mv %s.shortH %s/.\" )\n" % ( qryFileName, cDir )208 cmd_finish += "if not os.path.exists( \"%s/%s.shortHlink\" ):\n" % ( cDir, qryFileName )209 cmd_finish += "\tos.system( \"mv %s.shortHlink %s/.\" )\n" % ( qryFileName, cDir )210 cmd_finish += "if not os.path.exists( \"%s/%s.initOrder\" ):\n" % ( cDir, qryFileName )211 cmd_finish += "\tos.system( \"mv %s.initOrder %s/.\" )\n" % ( qryFileName, cDir )212 cLauncher.runSingleJob( cmd_start, cmd_finish )213 cLauncher.endRun()214 if config.get("classif_consensus","clean") == "yes":215 cLauncher.clean( acronym )216 jobdb.close()217 else:218 prg = os.environ["REPET_PATH"] + "/bin/shortenSeqHeader.py"219 cmd = prg220 cmd += " -i %s" % ( qryFileName )221 cmd += " -p %s" % ( "qry" )222 lCmds.append(cmd)223 224 cmd = prg225 cmd += " -i %s" % ( sbjFileName )226 cmd += " -p %s" % ( "sbj" )227 lCmds.append(cmd)228 if not useCluster:229 for c in lCmds:230 pL.launch( prg, c )231 else:232 acronym = "shortenSeqHeader"233 groupid = "rmvRedundancy_SubjectNotEqualQuery_shortenSeqHeader"234 jobdb = RepetJob( cfgFileName = configFileName )235 cLauncher = Launcher( jobdb, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid, acronym )236 cLauncher.beginRun()237 cLauncher.job.jobname = acronym238 cmd_start = ""239 cmd_start += "os.system( \"ln -s %s/%s .\" )\n" % ( cDir, qryFileName )240 cmd_start += "os.system( \"ln -s %s/%s .\" )\n" % ( cDir, sbjFileName )241 for c in lCmds:242 cmd_start += "log = os.system( \""243 cmd_start += c244 cmd_start += "\" )\n"245 cmd_finish = "if not os.path.exists( \"%s/%s.shortH\" ):\n" % ( cDir, qryFileName )246 cmd_finish += "\tos.system( \"mv %s.shortH %s/.\" )\n" % ( qryFileName, cDir )247 cmd_finish += "if not os.path.exists( \"%s/%s.shortHlink\" ):\n" % ( cDir, qryFileName )248 cmd_finish += "\tos.system( \"mv %s.shortHlink %s/.\" )\n" % ( qryFileName, cDir )249 cmd_finish += "if not os.path.exists( \"%s/%s.shortH\" ):\n" % ( cDir, sbjFileName )250 cmd_finish += "\tos.system( \"mv %s.shortH %s/.\" )\n" % ( sbjFileName, cDir )251 cmd_finish += "if not os.path.exists( \"%s/%s.shortHlink\" ):\n" % ( cDir, sbjFileName )252 cmd_finish += "\tos.system( \"mv %s.shortHlink %s/.\" )\n" % ( sbjFileName, cDir )253 cLauncher.runSingleJob( cmd_start, cmd_finish )254 cLauncher.endRun()255 if config.get("classif_consensus", "clean") == "yes":256 cLauncher.clean( acronym )257 jobdb.close()258 259 #--------------------------------------------------------------------------260 # case not in parallel261 if useCluster == False:262 # run Blaster263 prg = os.environ["REPET_PATH"] + "/bin/blaster"264 cmd = prg265 cmd += " -q %s.shortH" % ( qryFileName )266 cmd += " -s %s.shortH" % ( sbjFileName )267 cmd += " -a"268 cmd += " -I %i" % ( int(100*thresIdentity) )269 cmd += " -L %i" % ( lengthFilter )270 cmd += " -E %s" % ( threshEvalue )271 cmd += " -B %s.shortH_vs_%s.shortH" % ( qryFileName, sbjFileName )272 pL.launch( prg, cmd )273 # run Matcher274 prg = os.environ["REPET_PATH"] + "/bin/matcher"275 cmd = prg276 cmd += " -m %s.shortH_vs_%s.shortH.align" % ( qryFileName, sbjFileName )277 cmd += " -q %s.shortH" % ( qryFileName )278 cmd += " -s %s.shortH" % ( sbjFileName )279 cmd += " -j"280 cmd += " -a"281 pL.launch( prg, cmd )282 #--------------------------------------------------------------------------283 284 # case in parallel285 elif useCluster == True:286 # run Blaster + Matcher287 prg = os.environ["REPET_PATH"] + "/bin/launchBlasterMatcherPerQuery.py"288 cmd = prg289 cmd += " -q %s.shortH" % ( qryFileName )290 cmd += " -s %s.shortH" % ( sbjFileName )291 cmd += " -Q '%s'" % ( queue )292 cmd += " -d %s" % ( os.getcwd() )293 cmd += " -C %s" % ( configFileName )294 cmd += " -n %i" % ( maxNbJobs )295 cmd += " -B \"-a -I %s -L %s -E %s\"" % ( int(100*thresIdentity), lengthFilter, threshEvalue )296 cmd += " -M \"%s\"" % ( "-j -a" )297 cmd += " -Z tab"298 if clean == True:299 cmd += " -c"300 cmd += " -v %i" % ( verbose - 1 )301 pL.launch( prg, cmd )302 #--------------------------------------------------------------------------303 # filter the resulting 'tab' file304 prg = os.environ["REPET_PATH"] + "/bin/filterOutMatcher.py"305 cmd = prg306 cmd += " -q %s.shortH" % ( qryFileName )307 if sbjFileName != qryFileName:308 cmd += " -s %s.shortH" % ( sbjFileName )309 cmd += " -m %s.shortH_vs_%s.shortH.align.match.tab" % ( qryFileName, sbjFileName )310 cmd += " -o %s.shortH.filtered" % ( qryFileName )311 cmd += " -i %f" % ( thresIdentity )312 cmd += " -l %f" % ( thresLength )313 cmd += " -L %s" % ( logFileName )314 cmd += " -v %i" % ( verbose )315 316 if not useCluster:317 pL.launch( prg, cmd )318 else:319 groupid = "rmvRedundancy_filterOutMatcher"320 acronym = "filterOutMatcher"321 jobdb = RepetJob( cfgFileName = configFileName )322 cLauncher = Launcher( jobdb, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid, acronym )323 cLauncher.beginRun()324 cLauncher.job.jobname = acronym325 cmd_start = ""326 cmd_start += "os.system( \"ln -s %s/%s.shortH .\" )\n" % ( cDir, qryFileName )327 if sbjFileName != qryFileName:328 cmd_start += "os.system( \"ln -s %s/%s.shortH .\" )\n" % ( cDir, sbjFileName )329 cmd_start += "os.system( \"ln -s %s/%s.shortH_vs_%s.shortH.align.match.tab .\" )\n" % ( cDir, qryFileName, sbjFileName )330 cmd_start += "log = os.system( \""331 cmd_start += cmd332 cmd_start += "\" )\n"333 cmd_finish = "if not os.path.exists( \"%s/%s.shortH.filtered\" ):\n" % ( cDir, qryFileName )334 cmd_finish += "\tos.system( \"mv %s.shortH.filtered %s/.\" )\n" % ( qryFileName, cDir )335 cmd_finish += "if not os.path.exists( \"%s/%s.shortH_vs_%s.shortH.align.match.tab\" ):\n" % ( cDir, qryFileName, sbjFileName )336 cmd_finish += "\tos.system( \"mv %s.shortH_vs_%s.shortH.align.match.tab %s/.\" )\n" % ( qryFileName, sbjFileName, cDir )337 cmd_finish += "if not os.path.exists( \"%s/%s\" ):\n" % ( cDir, logFileName )338 cmd_finish += "\tos.system( \"mv %s %s/.\" )\n" % ( logFileName, cDir )339 cLauncher.runSingleJob( cmd_start, cmd_finish )340 cLauncher.endRun()341 if config.get("classif_consensus", "clean") == "yes":342 cLauncher.clean( acronym )343 jobdb.close()344 345 # retrieve initial headers346 prg = os.environ["REPET_PATH"] + "/bin/ChangeSequenceHeaders.py"347 cmd = prg348 cmd += " -i %s.shortH.filtered" % ( qryFileName )349 cmd += " -f fasta"350 cmd += " -s 2"351 cmd += " -l %s.shortHlink" % ( qryFileName )352 cmd += " -o %s" % ( outFileName )353 354 if not useCluster:355 pL.launch( prg, cmd )356 else:357 groupid = "rmvRedundancy_ChangeSequenceHeaders"358 acronym = "ChangeSequenceHeaders"359 jobdb = RepetJob( cfgFileName = configFileName )360 cLauncher = Launcher( jobdb, os.getcwd(), "", "", cDir, tmpDir, "jobs", queue, groupid, acronym )361 cLauncher.beginRun()362 cLauncher.job.jobname = acronym363 cmd_start = ""364 cmd_start += "os.system( \"ln -s %s/%s.shortH.filtered .\" )\n" % ( cDir, qryFileName )365 cmd_start += "os.system( \"ln -s %s/%s.shortHlink .\" )\n" % ( cDir, qryFileName )366 cmd_start += "log = os.system( \""367 cmd_start += cmd368 cmd_start += "\" )\n"369 cmd_finish = "if not os.path.exists( \"%s/%s\" ):\n" % ( cDir, outFileName )370 cmd_finish += "\tos.system( \"mv %s %s/.\" )\n" % ( outFileName, cDir )371 cLauncher.runSingleJob( cmd_start, cmd_finish )372 cLauncher.endRun()373 if config.get("classif_consensus", "clean") == "yes":374 cLauncher.clean( acronym )375 jobdb.close()376 # future improvement: give file '.shortHlink' to 'filterOutMatcher.py' so that it saves the information about which match removed which query, with the true headers377 os.system( "mv %s .." % ( outFileName ) )378 os.chdir( ".." )379 if clean == True:380 shutil.rmtree( uniqTmpDir )381 logging.info( "finished" )382 if verbose > 0:383 print "END %s (%s)" % ( sys.argv[0].split("/")[-1],384 time.strftime("%m/%d/%Y %H:%M:%S") )385 sys.stdout.flush()386 return 0387if __name__ == "__main__":...
optional_rhseqv2_wrapper.py
Source:optional_rhseqv2_wrapper.py
1import os23## USAGE ##4# python optional_rhseqv2_wrapper5# optional wrapper for running the rhseq pipeline from poolCount to mwu analysis with one command6# generates, prints (optional), and runs (optional) a command for all the rhseq scripts with their current paramters7# call this wrapper from the folder where output is intended)89##PARAMETERS##10printCommand=True11runCommand=False1213scriptDir='/usr2/people/mabrams/scripts/' #the location where the rhseqv2 scripts are saved14py3='python' #the call for python at the start of the script151617poolCountFile='poolCount.txt'#name/path to the first infile (the poolCount from the Coradetti et al. RBseq pipeline RBseq_Count_Barcodes script v1.1.4 (no changes))181920##RUN##21if __name__ == '__main__':22 command=''2324 cmd_start=py3+' '+scriptDir25 outDir='./' 26 cmd_mid=' '+outDir+' '27 28 command=cmd_start+'convert_poolcount_to_fastqpooledreadsclean_rhseqv2.py'+cmd_mid+poolCountFile+';'29 command+=cmd_start+'2total_reads_and_normalize_rhseqv2.py'+cmd_mid+'./*fastq_pooled_reads_clean;'30 command+=cmd_start+'3remove_NC_and_plasmid_inserts_rhseqv2.py'+cmd_mid+'./*.normalized_pooled_reads;'31 command+=cmd_start+'4reformat_single_techrep_rhseqv2.py'+cmd_mid+'./*.normalized_pooled_reads_coding;'32 command+=cmd_start+'5combine_bioreps_rhseqv2.py'+cmd_mid+'*.normalized_averaged_techreps;'33 command+=cmd_start+'6filter_inserts_rhseqv2.py'+cmd_mid+'*.normalized_averaged_bioreps;'34 command+=cmd_start+'7fitness_ratios_rhseqv2.py'+cmd_mid+'*.filtered_inserts;'35 command+=cmd_start+'8organize_and_filter_genes_rhseqv2.py'+cmd_mid+'*.insert_ratios;'36 command+=cmd_start+'9mann_whitney_u_rhseqv2.py'+cmd_mid+'*.filtered_gene_inserts;'37 command+=cmd_start+'10effect_size_rhseqv2.py'+cmd_mid+'*.filtered_gene_inserts'+'*.mwu_test_results;'383940 if printCommand==True:41 print(command)42 if runCommand==True:43 os.system(command)4445 464748
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