def run( self ):
"""
Run the program.
"""
self.start()
lInitHeaders = FastaUtils.dbHeaders( self.getInputFile(), self.getVerbosityLevel()-1 )
csh = ChangeSequenceHeaders()
csh.setInputFile( self.getInputFile() )
csh.setFormat( "fasta" )
csh.setStep( 1 )
csh.setPrefix( "seq" )
csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
csh.setOutputFile( "%s.shortH" % ( self.getInputFile() ) )
csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
csh.run()
bsDB = BioseqDB( "%s.shortH" % ( self.getInputFile() ) )
bsDB.upCase()
bsDB.save( "%s.shortHtmp" % ( self.getInputFile() ) )
del bsDB
os.rename( "%s.shortHtmp" % ( self.getInputFile() ),
"%s.shortH" % ( self.getInputFile() ) )
self.setProgramCommandLine()
cmd = self.getProgramCommandLine()
if self.getVerbosityLevel() > 0:
print "LAUNCH: %s" % ( cmd )
sys.stdout.flush()
exitStatus = os.system( cmd )
if exitStatus != 0:
string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
print string
sys.exit(1)
csh.setInputFile( "%s.shortH.fa_aln" % ( self.getInputFile() ) )
csh.setFormat( "fasta" )
csh.setStep( 2 )
csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
csh.setOutputFile( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
csh.run()
absDB = AlignedBioseqDB( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
outFileHandler = open( self.getOutputFile(), "w" )
for header in lInitHeaders:
bs = absDB.fetch( header )
bs.upCase()
bs.write( outFileHandler )
outFileHandler.close()
os.remove( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
self.end()
print "prepare MSP file"; sys.stdout.flush()
prg = os.environ["REPET_PATH"] + "/bin/align2recon.py"
cmd = prg
cmd += " -i %s" % ( alignFileName )
cmd += " -o %s_MSP_file" % ( projectName )
cmd += " -v %i" % ( verbose - 1 )
returnStatus = os.system( cmd )
if returnStatus != 0:
msg = "ERROR: '%s' returned '%i'" % ( prg, returnStatus )
sys.stderr.write( "%s\n" % ( msg ) )
sys.exit(1)
if verbose > 0:
print "prepare seq file"; sys.stdout.flush()
lSeqNames = FastaUtils.dbHeaders( faFileName, verbose - 1 )
lSeqNames.sort()
seqListFile = open( projectName + "_seq_list", "w" )
seqListFile.write( str(len(lSeqNames)) + "\n" )
for seqName in lSeqNames:
seqListFile.write( ">%s\n" % ( seqName ) )
seqListFile.close()
if verbose > 0:
print "Recon is running..."; sys.stdout.flush()
prg = "recon.pl"
cmd = prg
cmd += " %s_seq_list" % ( projectName )
cmd += " %s_MSP_file" % ( projectName )
cmd += " 1"
