def main(args,maxMismatch=0,seedLen=36):
for f in args:
bowtieFile,bowtiePath = mystemp(suffix='.bowtie')
fStub,fExt = os.path.splitext(f)
oFile = safeOFW('.'.join((fStub,'Hg18rm',fExt[1:])),'w')
print os.curdir
try:
subprocess.call(['bowtie', '-f','-l',str(seedLen),'-n',str(maxMismatch),
hg18db, f, bowtiePath])
humanQrys =B.readTitleSet(bowtiePath)
if len(humanQrys)==0:
raise RuntimeError, "No Alignments found"
for rec in fasta.generalIterator(f):
if rec.title in humanQrys:
continue
else:
print >> oFile, rec
oFile.close()
except BaseException:
os.unlink(oFile.name)
print '%s -failed' %f
raise
finally:
os.unlink(bowtiePath)
return 0
def main(args):
for f in args:
mbrFile,mbrPath = mystemp(suffix='.mbr')
fStub,fExt = os.path.splitext(f)
oFile = safeOFW('.'.join((fStub,'Hg18rm',fExt[1:])),'w')
print os.curdir
try:
subprocess.call(['megablast', '-m8', '-i',f,
'-d', hg18db,'-o', mbrPath])
humanQrys =B.m8TitleSet(mbrPath,qrySet=True)
for rec in fasta.generalIterator(f):
if len(humanQrys)==0:
break
if rec.title in humanQrys:
continue
else:
print >> oFile, rec
oFile.close()
except BaseException:
os.unlink(oFile.name)
print '%s -failed' %f
raise
finally:
os.unlink(mbrPath)
return 0
def main(sysargs=[]):
# short usage message
oneLineUsage = "Usage: %prog [options] <input files>"
# set a long desccription for the help message
description=("Add reverse complement fasta records to Fasta file(s). "
"Use '-' to read from STDIN.")
op = optparse.OptionParser(
oneLineUsage,description=description,
version="%prog " + '.'.join([str(x) for x in __version__]))
# OPTION DEFINITIONS
op.add_option('-o','--outputfile',dest="outFileName",default='-',
help="name of output file. '-' means: STDOUT")
op.add_option('-c','--clobber',action="store_true", default=False,
dest="clobber", help="allow output file to be overwritten.")
# all options should be defined above here
### Don't Change In Box ###################
# #
# OPTION PATCHING #
# add defaults to help messages #
# #
for o in op.option_list: #
if o.type == None: #
continue #
if o.help == None: #
o.help = "Default: %default" #
else: #
o.help+= " Default: %default" #
#
#
# #
# OPTION PARSING #
(opts,args) = op.parse_args(sysargs) #
# #
# option values are available as attrs #
# of the opts object, e.g. opts.myClobber #
# #
# args is a list of the balance of the #
# command line #
###########################################
# OPTION CHECKING
try:
# (check an opt) tileSizes = [int(x) for x in opts.tileSizesL.split(',') if len(x)>0]
outFile = utils.safeOFW(opts.outFileName,clobber=opts.clobber) # open the output file
except Exception, eData:
print >> sys.stderr, ("\nOption Error: %s\n" %eData.message)
print >> sys.stderr, op.format_help()
return 1
def cluster(self,outFile,log2transform=True):
"""
"""
if type(outFile) in StringTypes:
oFile=safeOFW(outFileName)
else:
oFile=outFile
print >> oFile, '\t'.join(['LOCUS','NAME']+self.sampleNames)
for row in self.sampleIdNameData(log2transform):
if row[2:].count('') < len(row[2:]):
print >> oFile, '\t'.join(row)
oFile.close()
def main(sysargs=[]):
# short usage message
oneLineUsage = "Usage: %prog [options] <input files>"
description="""
Checks for binary zeros in files. Exit status is non zero if zeros
are detected. Checking a file is stopped as soon as a zero is found.
Gzip'ed files are accepted, and unzipped on the fly. '-' indicates
that standard input should be checked.
"""
op = optparse.OptionParser(
oneLineUsage,description=description,
version="%prog " + '.'.join([str(x) for x in __version__]))
# OPTION DEFINITIONS
op.add_option('-o','--outputfile',dest="outFileName",default='-',
help="name of output file. '-' means: STDOUT")
op.add_option('-c','--clobber',action="store_true", default=False,
dest="clobber", help="allow output file to be overwritten.")
op.add_option('-a', '--append', action="store_true", default=False,
dest="append", help="append to output file..")
# all options should be defined above here
# (you don't have to define version or help)
# add defaults to help messages
for o in op.option_list:
if o.type == None:
continue
if o.help == None:
o.help = "Default: %default"
else:
o.help+= " Default: %default"
# OPTION PARSING
(opts,args) = op.parse_args(sysargs)
# OPTION CHECKING
try:
# (check an opt)
outFile = utils.safeOFW(opts.outFileName,
append=opts.append,clobber=opts.clobber) # open the output file
except Exception, eData:
print >> sys.stderr, ("\nOption Error: %s\n" %eData.message)
print >> sys.stderr, op.format_help()
return 1
def main(sysargs=[]):
# short usage message
oneLineUsage = "Usage: %prog [options] <input files>"
# set a long desccription for the help message
description=None
op = optparse.OptionParser(
oneLineUsage,description=description,
version="%prog " + '.'.join([str(x) for x in __version__]))
# OPTION DEFINITIONS
op.add_option('-d','--drop-dup', dest="dropDup",default=False,
action="store_true",
help="remove duplicate sequences from output")
op.add_option('-o','--outputfile',dest="outFileName",default='-',
help="name of output file. '-' means: STDOUT")
op.add_option('-c','--clobber',action="store_true", default=False,
dest="clobber", help="allow output file to be overwritten.")
op.add_option('-a', '--append', action="store_true", default=False,
dest="append", help="append to output file..")
# all options should be defined above here
# (you don't have to define version or help)
# add defaults to help messages
for o in op.option_list:
if o.type == None:
continue
if o.help == None:
o.help = "Default: %default"
else:
o.help+= " Default: %default"
# OPTION PARSING
(opts,args) = op.parse_args(sysargs)
# OPTION CHECKING
try:
# (check an opt) tileSizes = [int(x) for x in opts.tileSizesL.split(',') if len(x)>0]
outFile = utils.safeOFW(opts.outFileName,
append=opts.append,clobber=opts.clobber) # open the output file
except Exception, eData:
print >> sys.stderr, ("\nOption Error: %s\n" %eData.message)
print >> sys.stderr, op.format_help()
return 1
def main(sysargs):
op = optparse.OptionParser("Usage: %prog [options] <fasta files>",
version=__version__)
op.add_option('-t','--tilesizes',dest="tileSizesL", default="60",
help="comma seperated list of tile sizes to generate. e.g. '50,70'.")
op.add_option('-s','--shift',default=25,type='int',dest="shift",
help="Start position offset" )
op.add_option('-c','--clobber',action="store_true", default=False,
dest="clobber", help="allow output file to be overwritten.")
op.add_option('-E','--endtile',action="store_false", default=True,
dest="endtile", help="Suppress generation of an tile that covers the"
" last base in each recrod regardless of the -s and -t settings.")
op.add_option('-o','--outputfile',dest="outFileName",default='-',
help="name of output file. '-' means: STDOUT")
op.add_option('-P','--permissiveTitles',action="store_true", default=False,
dest="nonGiTitles",
help="allow non-gi fasta titles when calculating tile titles")
for o in op.option_list:
if o.help == None:
o.help = "Default: %default"
else:
o.help+= " Default: %default"
(opts,args) = op.parse_args(sysargs)
if opts.nonGiTitles:
tileTitleCallback = fasta.generalTileTitle
else:
tileTitleCallback = fasta.giTileTitle
try:
tileSizes = [int(x) for x in opts.tileSizesL.split(',') if len(x)>0]
outFile = utils.safeOFW(opts.outFileName,clobber=opts.clobber)
except Exception, eData:
print >> sys.stderr, ("\nOption Error: %s\n" %eData.message)
print >> sys.stderr, op.format_help()
return 1
def main(sysargs):
usageStr = __doc__
epilog = ""
op = optparse.OptionParser(usageStr, version=__version__)
#
# OPTION DEFINITIONS
#
op.add_option("-t", "--tablesuffix", default="", help="Hsp table suffix")
op.add_option("-c", "--clobber", action="store_true", default=False, help="allow output file to be overwritten.")
op.add_option("-l", "--logfile", default="-", help="name of log file. '-' means: STDOUT")
#
# OPTION PATCHING
#
# add "defaults" to help messages
for o in op.option_list:
if o.type != None or o.action.startswith("store_"):
if o.help == None:
o.help = "Default: %default"
else:
o.help += " Default: %default"
# call the parser
(opts, m8files) = op.parse_args(sysargs)
#
# OPTION CHECKING
#
# Example of option checking beyond what parse_args does:
# (Note that parse_args can do some basic type checking
# and conversion.)
try:
outFile = utils.safeOFW(opts.logfile, clobber=opts.clobber)
except Exception, eData:
print >>sys.stderr, ("\nOption Error: %s\n" % eData.message)
print >>sys.stderr, op.format_help()
return 1
def processFiles(files, clobber=False):
for f in files:
outF = safeOFW(f + ".dG", clobber=clobber)
for hsp in B.xmlBlast2energy(f):
print >> outF, "\t".join([str(x) for x in [hsp[0], hsp[1], hsp[-1]]])
return 0
def main(sysargs=[]):
# short usage message
oneLineUsage = "Usage: %prog [options] <sequence files>"
# set a long desccription for the help message
description=(
"Takes files containing reads (raw sequence with no title info)"
" and combines them into a fasta file. The fasta titles are"
" derived from the file names."
)
op = optparse.OptionParser(
oneLineUsage,description=description,
version="%prog " + '.'.join([str(x) for x in __version__]))
# OPTION DEFINITIONS
op.add_option('-o','--outputfile',dest="outFileName",default=defaultOutName,
help="name of output file. '-' means: STDOUT")
op.add_option('-c','--clobber',action="store_true", default=False,
dest="clobber", help="allow output file to be overwritten.")
op.add_option('-w','--width',dest="fmtWidth", default=defaultFastaWidth,
help="formatted width of output fasta records.")
op.add_option('-s','--spaceChar',dest="spaceChar",default=defaultSpaceChar,
help="replace title spaces with this character/string")
op.add_option('-P','--useFullPaths',action="store_true",
dest="useFullPaths",default=False,
help="include pathnames in titles")
# all options should be defined above here
# OPTION PATCHING
# add defaults to help messages
for o in op.option_list:
if o.type == None:
continue
if o.help == None:
o.help = "Default: %default"
else:
o.help+= " Default: %default"
# OPTION PARSING
(opts,args) = op.parse_args(sysargs) # call the parser
# option values are available as attributes of the opts object
# e.g. opts.myClobber
# args is a list of the balance of the command line
# OPTION CHECKING
# Example of option checking beyond what parse_args does:
# (Note that parse_args can do some basic type checking
# and conversion.)
try:
# (check an opt) tileSizes = [int(x) for x in opts.tileSizesL.split(',') if len(x)>0]
outFile = utils.safeOFW(opts.outFileName,clobber=opts.clobber) # open the output file
except Exception, eData:
print >> sys.stderr, ("\nOption Error: %s\n" %eData.message)
print >> sys.stderr, op.format_help()
return 1
def main(sysargs=[]):
"""
"""
oneLineUsage = "Usage: %prog [options] <input fasta file>"
# set a long desccription for the help message
description = """This program makes a multiprocess (RPC) screener to remove
redundant sequence from a fastafile.
The output file is named identityScreen_Rpyc.py.
"""
op = optparse.OptionParser(
oneLineUsage, description=description, version="%prog " + ".".join([str(x) for x in __version__])
)
# OPTION DEFINITIONS
op.add_option(
"-o",
"--outputfile",
dest="outFileName",
default="identityScreen_Rpyc.py",
help="name of output file. '-' means: STDOUT",
)
op.add_option(
"-c",
"--clobber",
action="store_true",
default=False,
dest="clobber",
help="allow output file to be overwritten.",
)
op.add_option("-n", "--slice-names", dest="faNameFile", help="Name of file that will hold the slice names")
op.add_option(
"-S",
"--slice-size",
dest="sliceSize",
type="int",
default=sliceSize,
help="maximum size, in bytes, of each slice file",
)
op.add_option("-C", "--slice-count", dest="sliceCount", type="int", default=sliceSize, help="number of slices")
# add defaults to help messages
for o in op.option_list:
if o.type == None:
continue
if o.help == None:
o.help = "Default: %default"
else:
o.help += " Default: %default"
# OPTION PARSING
(opts, args) = op.parse_args(sysargs)
try:
if opts.sliceSize is None and opts.sliceCount is None:
raise Exception, "sliceCount (-C) or sliceSize (-S) must be set."
if len(args) != 1:
raise Exception, "Input fasta file must me specified."
outFile = utils.safeOFW(opts.outFileName, append=False, clobber=opts.clobber) # open the output file
except Exception, eData:
# raise
print >>sys.stderr, ("\nUsage Error: %s\n" % eData.message)
print >>sys.stderr, op.format_help()
return 1
## print >> sys.stderr, ("\nWrong number of files or arguments: "
## "%s found (expected max of %s)"
## % (len(args), maxArgs))
## argProblem = True
## elif len(args) < minArgs:
## print >> sys.stderr, ("\nWrong number of files or arguments: "
## "%s found (expected min of %s)"
## % (len(args),minArgs))
## argProblem = True
## if argProblem:
## print >> sys.stderr, op.format_help()
## return 1
oFile = utils.safeOFW(opts.outFileName, clobber=opts.clobber)
somethingUsefull(args, oFile)
return 0 # we did it!
def somethingUsefull(args, oFile):
for f in args:
for rec in fasta.generalIterator(f):
if fasta.isAllDRNA(rec.sequence):
print >> oFile, rec
else:
n = 0
for uaSeq in fasta.expandAmbiguousSequence(rec.sequence):
uaTitle = rec.title + "|ua%s" % n
def main(args):
parser = OptionParser(('usage: %prog [options] '
'<qualifier to use as gene name>'))
parser.add_option('-g', '--gi', dest='gi', type='int',
help='gi of the genbank record to analyze.')
parser.add_option('-r', '--record', dest='record', type='string',
help='read genbank record from FILE',
metavar='FILE')
parser.add_option('-o', '--output', dest="output",
help='name of output file.')
parser.add_option('-c', '--clobber', dest="clobber",
help='Clobber the output files.',
action='store_true', default=False)
(options, args) = parser.parse_args(args)
if not options.gi and not options.record:
print >> sys.stderr, 'Usage error: a record file (-r) or ' + \
'a gi (-g) is required'
print >> sys.stderr, parser.format_help()
sys.exit(1)
if options.output:
filenameOut = options.output
else:
if options.record:
filenameOut = '%s' % options.record
else:
filenameOut = '%s' % options.gi
if len(args) < 2:
print >> sys.stderr, 'Qualifier name is required'
print >> sys.stderr, parser.format_help()
sys.exit(1)
if options.record:
record = genbank.Record(file(options.record))
else:
record = giInfo.GiRecord(options.gi, True)
qualifierName = args[1]
fastaFh = safeOFW('%s.fasta' % filenameOut,
clobber=options.clobber)
print >> fastaFh, record.fasta()
fastaFh.close()
genesFh = safeOFW('%s.genes.fasta' % filenameOut,
clobber=options.clobber)
genes = []
for feature in record.features():
if len(feature.location.regions) != 1:
continue
if feature.type != 'gene':
continue
region = feature.location.regions[0]
seq = record.sequence[region.start - 1:region.end]
seq = seq.upper()
if region.complement:
seq = genbank.reverseComplement(seq)
if feature.qualifiers.has_key(qualifierName):
feat_name = feature.qualifiers[qualifierName]
else:
print >> sys.stderr, ("Feature doesn't have qualifier "
"'%s'.\nQualifiers: %s" %
(qualifierName, feature.qualifiers))
continue
print >> genesFh, fasta.Record(title=feat_name, sequence=seq)
print >> genesFh, ''
genesFh.close()
def main(sysargs=[]):
# short usage message
oneLineUsage = "Usage: %prog [options] <input file>"
# set a long desccription for the help message
description = (
"Extract random records or subsequences from a input fasta/fastq file.\n"
"Input file can be STDIN; specified as '-'.\n"
)
op = optparse.OptionParser(
oneLineUsage, description=description, version="%prog " + ".".join([str(x) for x in __version__])
)
# Output Control
op.add_option("-o", "--outputfile", dest="outFileName", default="-", help="name of output file. '-' means: STDOUT")
op.add_option(
"-c",
"--clobber",
action="store_true",
default=False,
dest="clobber",
help="allow output file to be overwritten.",
)
op.add_option("-a", "--append", action="store_true", default=False, dest="append", help="append to output file..")
# Subsequence control
op.add_option(
"-l",
"--length",
dest="ssLen",
type="int",
default=None,
action="store",
help="length of subsequences. " "If None, the complete input record is output.",
)
op.add_option(
"-n",
"--number",
dest="recNumber",
type="int",
default=1,
action="store",
help="number of output records. " "Set to 0 for no limit",
)
op.add_option(
"-e", "--excludePat", dest="exRE", default=None, action="store", help="exclude sequences that match regex"
)
# all options should be defined above here
# (you don't have to define version or help)
# add defaults to help messages
for o in op.option_list:
if o.type == None:
continue
if o.help == None:
o.help = "Default: %default"
else:
o.help += " Default: %default"
# OPTION PARSING
(opts, args) = op.parse_args(sysargs)
if opts.recNumber == 0:
opts.recNumber = None
# OPTION CHECKING
try:
# (check an opt) tileSizes = [int(x) for x in opts.tileSizesL.split(',') if len(x)>0]
outFile = utils.safeOFW(opts.outFileName, append=opts.append, clobber=opts.clobber) # open the output file
except Exception, eData:
print >>sys.stderr, ("\nOption Error: %s\n" % eData.message)
print >>sys.stderr, op.format_help()
return 1
def main(sysargs=[]):
# short usage message
oneLineUsage = "Usage: %prog [options] <input files>"
# set a long desccription for the help message
description=None
op = optparse.OptionParser(
oneLineUsage,description=description,
version="%prog " + '.'.join([str(x) for x in __version__]))
# OPTION DEFINITIONS
op.add_option('-o','--outputfile',dest="outFileName",default='-',
help="name of output file. '-' means: STDOUT")
op.add_option('-c','--clobber',action="store_true", default=False,
dest="clobber", help="allow output file to be overwritten.")
# Below are some examples of setting up options
# Note the above line gives you -h, --help, --version
# and an error message if an unspecified option is given.
# for more see: http://docs.python.org/library/optparse.html#defining-options
##
## op.add_option('-t','--tilesizes',dest="tileSizesL", default="60",
## help="comma seperated list of tile sizes to generate. e.g. '50,70'.")
## op.add_option('-s','--shift',default=25,type='int',dest="shift",
## help="Start position offset" )
## op.add_option('-E','--endtile',action="store_false", default=False,
## dest="endtile", help="Suppress generation of an tile that covers the"
## " last base in each recrod regardless of the -s and -t settings.")
##
# all options should be defined above here
### Don't Change In Box ###################
# #
# OPTION PATCHING #
# add defaults to help messages #
# #
for o in op.option_list: #
if o.type == None: #
continue #
if o.help == None: #
o.help = "Default: %default" #
else: #
o.help+= " Default: %default" #
#
#
# #
# OPTION PARSING #
(opts,args) = op.parse_args(sysargs) #
# #
# option values are available as attrs #
# of the opts object, e.g. opts.myClobber #
# #
# args is a list of the balance of the #
# command line #
###########################################
# OPTION CHECKING
# Option checking beyond what parse_args does:
# (Note that parse_args can do some basic
# type checking and conversion.)
try:
# (check an opt) tileSizes = [int(x) for x in opts.tileSizesL.split(',') if len(x)>0]
outFile = utils.safeOFW(opts.outFileName,clobber=opts.clobber) # open the output file
except Exception, eData:
print >> sys.stderr, ("\nOption Error: %s\n" %eData.message)
print >> sys.stderr, op.format_help()
return 1