def main():
parser = optparse.OptionParser()
parser.add_option( '-i', '--inputfile',
dest='inputfilename',
help='fasta file in which selenoproteins should be looked for.',
metavar='FILE' )
parser.add_option( '-o', '--outputfile',
dest='outputfilename',
help='fasta file containing the selenoproteins',
metavar='FILE' )
parser.add_option( '-v', '--verbose',
dest='verbosity',
help='verbosity level : 0=none ; 1=standard ; 2=detailed ; 3=full',
metavar='INTEGER' )
parser.set_defaults( verbosity = '1' )
(options, args) = parser.parse_args()
stdoutflag = False
verbosity = int( options.verbosity )
if options.inputfilename:
inputfilenames = options.inputfilename.split(',')
infiles = []
for i in inputfilenames:
infiles.append( open( i, 'r' ) )
else: sys.exit( 'You must provide an input filename.')
if options.outputfilename:
outfile = open( options.outputfilename, 'w' )
stdoutflag = True
else: outfile = sys.stdout
for f in infiles:
if verbosity >= 1:
print
print '>>> Searching for selenoproteins in file ' + f.name
print
if verbosity >= 2:
print '>>> Loading sequences ...'
sequences = FastaLib.loadSequences( f )
if verbosity >= 2:
print '>>> ... Done.'
print
if verbosity >= 2:
print '>>> Searching for U containing sequences ...'
selenoproteins = findSelenoproteins( sequences )
if verbosity >= 2:
print '>>> ... Done.'
print
FastaLib.saveSequences(selenoproteins, outfile)
for selP in selenoproteins:
if verbosity >= 3 and stdoutflag:
print selP.header.strip()
print selP.sequence.strip()
if verbosity >= 1:
print
print 'Found ' + str( len( selenoproteins ) ) + ' selenoproteins'
print
for i in infiles:
i.close()
outfile.close()
def main():
parser = optparse.OptionParser()
parser.add_option( '-i', '--inputfile',
dest='inputfilename',
help='file containing the alignments that will be used to build the PSSM using prepare_alignment_selenoprofiles.py.',
metavar='FILE' )
parser.add_option( '-r', '--datadir',
dest='datadir',
help='directory containing, for each familly FAM, a directory FAM.blast and a directory FAM.selenoprofiles.prep',
metavar='DIR' )
parser.add_option( '-o', '--outputfile',
dest='outputfilename',
help='base name used for outputs',
metavar='NAME' )
parser.add_option( '-a', '--n_core',
dest='ncore',
type='int',
help='number of cores to use during the various operations.',
metavar='INTEGER' )
parser.add_option( '-M', '--mafft',
action='store_true', dest='domafft', default=False,
help='do the mafft step.')
parser.add_option( '-T', '--trimal',
action='store_true', dest='dotrimal', default=False,
help='do the trimal step.')
parser.add_option( '-C', '--tcoffee',
action='store_true', dest='dotcoffee', default=False,
help='do the t_coffee step.')
parser.add_option( '-B', '--headers',
action='store_true', dest='doheaders', default=False,
help='do the addheaders step.')
parser.add_option( '-p', '--patternfile',
dest='patternfile',
help='pattern file to use if the -D option is used.',
metavar='FILE' )
parser.add_option( '-F', '--filter',
action='store_true', dest='dofilter', default=False,
help='do the filter step.')
parser.add_option( '-P', '--prepare',
action='store_true', dest='doprepal', default=False,
help='do the prepare_alignment_selenoprofiles step.')
parser.add_option( '-g', '--tag_threshold',
dest='tagthreshold',
type='float',
help='tag threshold to use if the -P or --prepare is used.',
metavar='FLOAT' )
parser.add_option( '-A', '--all',
action='store_true', dest='doall', default=False,
help='do all steps.')
parser.add_option( '-Y', '--dry',
action='store_true', dest='dryrun', default=False,
help="Prints the commands without executing them.")
parser.add_option( '-D', '--debug',
action='store_true', dest='debug', default=False,
help="Debug mode. Nothing is cleaned.")
parser.add_option( '-t', '--temp',
dest='temp',
help='set the temp folder to use.',
metavar='FOLDER' )
parser.add_option( '-v', '--verbose',
dest='verbosity',
type='int',
help='verbosity level : 0=none ; 1=standard ; 2=detailed ; 3=full',
metavar='INTEGER' )
parser.set_defaults( verbosity = 1,
ncore = 1,
tagthreshold = 0.5,
temp = '/tmp/',
patternfile = 'None' )
(options, args) = parser.parse_args()
if options.doall:
options.doheaders = True
options.dofilter = True
options.domafft = True
options.dotrimal = True
options.dotcoffee = True
infile = options.inputfilename
tmpinitfilename = genTempfilename(options.temp, 'ungapped_')
with open(infile, 'r') as iff:
tmpseqs = Fasta.loadSequences(iff)
with open(tmpinitfilename, 'w') as ugf:
for seq in tmpseqs:
removeGaps(seq).prints(ugf)
tmpinfile = tmpinitfilename
mafftoutfile = ''.join((options.outputfilename, '_mafft.fasta'))
trimaloutfile1 = ''.join((options.outputfilename, '_trimmed_native.fasta'))
trimaloutfile2 = ''.join((options.outputfilename, '_trimmed_spadded.fasta'))
trimaloutfile = trimaloutfile1
tcoffeeoutfile = ''.join((options.outputfilename, '_tcoffee.fasta'))
fullheadoutfile = ''.join((options.outputfilename, '.det.fasta'))
# patternfile = ''.join(('.'.join(options.inputfilename.split('.')[:2]), '.index.0'))
patternfile = options.patternfile
filteroutfile = ''.join((options.outputfilename, '.filt.fasta'))
ncore = options.ncore
verbosity = options.verbosity
temp = options.temp
addheaders = UtilityWrappers.AddFullHeadersWrapper2(tmpinfile,
fullheadoutfile,
patternfile)
filterseqs = UtilityWrappers.FilterWrapper(tmpinfile,
filteroutfile,
inverse=True,
titlematch=('PREDICTED', 'predicted', 'hypothetical'))
mafft = UtilityWrappers.MafftWrapper(tmpinfile,
mafftoutfile,
auto=True)
trimal = UtilityWrappers.TrimalWrapper(tmpinfile,
trimaloutfile1,
clusters=100)
tcoffee = UtilityWrappers.TcoffeeWrapper(trimaloutfile2,
tcoffeeoutfile,
ncore=ncore)
prepsp = UtilityWrappers.SelenoprofilesPreWrapper(tmpinfile,
options.outputfilename,
all=True,
tagthreshold=options.tagthreshold,
temp=temp)
try:
if options.dryrun:
print('\nThis is a dry run. Relaunch the command without the option -Y to do the actual stuff.\n')
## Add full headers
## if options.doheaders:
## addheader.infile = tmpinfile
## tmpinfile = fullheadoutfile
## if options.dryrun:
## print addheaders.cline
## else:
## if verbosity >= 1:
## sys.stderr.write('\n >>> Adding headers\n\n')
## addheaders.run()
## Filter out the 'fake' proteins
if options.dofilter:
time.sleep(0.5)
filterseqs.infile = tmpinfile
tmpinfile = filteroutfile
if options.dryrun:
print filterseqs.cline
else:
if verbosity >= 1:
sys.stderr.write('\n >>> Filtering out\n\n')
filterseqs.run()
## run mafft
numseqinmafftoutput = 0
if options.domafft:
time.sleep(0.5)
mafft.infile = tmpinfile
tmpinfile = mafftoutfile
if options.dryrun:
print mafft.cline
else:
if verbosity >= 1:
sys.stderr.write('\n >>> Running Mafft\n\n')
mafft.run()
with open(mafftoutfile, 'r') as mfo:
seqs = Fasta.loadSequences(mfo)
numseqinmafftoutput = len(seqs)
## run trimal
if options.dotrimal and numseqinmafftoutput > 200:
time.sleep(0.5)
trimal.infile = tmpinfile
tmpinfile = trimaloutfile1
if options.dryrun:
print trimal.cline
else:
if verbosity >= 1:
sys.stderr.write('\n >>> Running Trimal\n\n')
trimal.run()
if not options.dryrun and options.dotcoffee and options.dotrimal:
if verbosity >= 1:
sys.stderr.write('\n >>> Removing gaps\n\n')
ti = open(tmpinfile, 'r')
tmpinfile = trimaloutfile2
to = open(tmpinfile, 'w')
si = Fasta.loadSequences(ti)
ti.close()
refs = Fasta.SequenceList()
## saves the sequences with no gaps
for s in si:
refs.append(removeGaps(s))
Fasta.saveSequences(refs, to)
if options.dotrimal and numseqinmafftoutput > 200:
if verbosity >= 1:
sys.stderr.write('\n >>> Adding ommited selenoproteins\n')
## Gather the non intersecting proteins from the 2 files
diffSelenoproteins = spDiff( mafftoutfile,
trimaloutfile1 )
spDiffr = Fasta.SequenceList()
## remove gaps from selenoproteins
for s in diffSelenoproteins:
spDiffr.append(removeGaps(s))
## append to the file the selenoproteins that were not present
Fasta.saveSequences(spDiffr, to)
to.close()
## run t_coffee
if options.dotcoffee:
time.sleep(0.5)
tcoffee.infile = tmpinfile
tmpinfile = tcoffeeoutfile
if options.dryrun:
print tcoffee.cline
else:
if verbosity >= 1:
sys.stderr.write('\n >>> Running T_coffee\n\n')
tcoffee.run()
## Add full headers
if options.doheaders:
time.sleep(0.5)
addheaders.infile = tmpinfile
tmpinfile = fullheadoutfile
if options.dryrun:
print addheaders.cline
else:
if verbosity >= 1:
sys.stderr.write('\n >>> Adding headers\n\n')
addheaders.run()
## prepare alignments for selenoprofiles
if options.doprepal:
time.sleep(0.5)
prepsp.infile = tmpinfile
if options.dryrun:
print prepsp.cline
else:
if verbosity >= 1:
sys.stderr.write('\n >>> preparing for selenoprofiles\n\n')
prepsp.run()
except KeyboardInterrupt:
sys.exit('manual exit.')
finally:
if not options.debug:
if verbosity >= 2:
sys.stderr.write('\n >>> Removing temporary file ' + tmpinitfilename +'\n\n')
os.remove(tmpinitfilename)
