def addTaxonOptions(parser,defaults={},choices={}):
# get format and filterPct options from blastm8
addHitTableOptions(parser,defaults)
# specific to taxon parsing:
parser.add_option("-m", "--mapFile", dest="mapFile",
default=defaults.get("mapFile",None),
metavar="MAPFILE", help="Location of file containing table of with db hit name as first column and taxa or taxonids in second column. Defaults to '%s'" % (defaults.get("mapFile",None)))
parser.add_option("-p", "--parseStyle",
default=defaults.get("parseStyle",ACCS),
choices=[ACCS,GIS,ORGS,HITID,HITDESC],
help="What should be parsed from the hit table: accessions('accs'), 'gis', organsim names in brackets ('orgs'), the full hit name('hitid'), or the full hit description('hitdesc'). (defaults to '%s')" % (defaults.get("parseStyle",ACCS)))
parser.add_option("-C", "--countMethod", dest="countMethod", default=defaults.get("countMethod","first"), choices=choices.get('countMethod',('first','most','all','LCA','consensus')),
help="How to deal with counts from multiple hits. (first, most: can return multiple hits, LCA: MEGAN-like, rLCA: redistributed LCA, all: return every hit, consensus: return None unless all the same). Do not use most or consensus with more than one rank at a time. Default is %s" % (defaults.get("countMethod","first")),
metavar="COUNTMETHOD")
addTaxonomyDirOption(parser, defaults)
def main():
usage = "usage: %prog [OPTIONS] BLAST_FILE"
description = """
Take a blast result table and output a subset of hits based on the chosen filtering options. If more than one blast file given, use -O to get multiple output files, otherwise all output data will be concatenated into one output.
"""
# command line options
parser = OptionParser(usage, description=description, conflict_handler='resolve')
addHitTableOptions(parser, flags='all')
parser.add_option("-o", "--outfilenome", dest="outfilename", default=None,
metavar="OUTFILENAME", help="Write masked fasta output to OUTFILENAME.")
parser.add_option('-O', '--autoOutName', default=False,
action='store_true',
help="Automatically generate output file name from input name and options. Overridden by -o, cannot be used with data from STDIN.")
addUniversalOptions(parser)
(options, args) = parser.parse_args()
setupLogging(options,description)
if options.hitTableFormat=='last':
if options.hitTableSort=='evalue':
parser.error("The last format has no evalue to sort by, sorry")
# check that we have blast file as argument
if len(args) <= 1:
# input
if len(args) == 1:
infile = args[0]
logging.info("reading data from %s" % (infile))
instream = open(infile,'rU')
else:
infile = './stdin'
logging.info("reading data from STDIN")
instream=sys.stdin
# output
if options.outfilename is not None:
logging.info("Writing data to %s" % (options.outfilename))
outstream=open(options.outfilename,'w')
elif options.autoOutName:
outfile=getOutputFile(infile,options)
logging.info("Writing data to %s" % (outfile))
outstream=open(outfile,'w')
else:
logging.info("writing data to STDOUT")
outstream=sys.stdout
# filter
params=FilterParams.createFromOptions(options)
filterM8(instream,outstream,params)
else:
if not options.autoOutName:
if options.outfilename is not None:
logging.info("Writing data to %s" % (options.outfilename))
outstream=open(options.outfilename,'w')
else:
logging.info("writing data to STDOUT")
outstream=sys.stdout
for infilename in args:
logging.info("reading data from %s" % (infilename))
instream=open(infilename,'rU')
if options.autoOutName:
outstream=open(getOutputFile(infilename,options),'w')
# filter
params=FilterParams.createFromOptions(options)
filterM8(instream,outstream,params)
if options.autoOutName:
outstream.close()
instream.close()
def main():
usage = "usage: %prog [OPTIONS] INPUT_FILE(S)"
description = """
Takes an m8 blast and assigns each read to a pathway or gene family. Blast may be specified with -i or piped to STDIN.
"""
parser = OptionParser(usage, description=description)
parser.add_option("-i", "--inputfile", dest="infile",
metavar="INFILE", help="Read data table from INFILE"),
addIOOptions(parser)
parser.add_option('-O', "--outputStyle", default="cols",
choices=['cols','lines','python'],
help="How are multiple assignments displayed in output. By default ('cols'), multiple hits show up in multiple columns. The 'lines' option prints out a new line for each assignment. The 'python' option prints each assignment as a python string (in quotes) or a list of strings (in quotes, separted by commas, surrounded bya pair of sqaure brackets).")
parser.add_option("-m", "--mapFile", dest="mapFile",
metavar="MAPFILE", help="Location of file containing table of with db hit name as first column and geneIDs (Knumber) in second column.")
parser.add_option("-M", "--mapStyle", default='auto', choices=['auto','kegg','tab'],
help="What type of mapping file are you using: simple tab separated list of IDs and kos, or the genes_ko.list file from KEGG (which adds ko: to the K numbers and can have multiple records for each gene id). By default, this script will inspect the file name and guess, but you can force either 'kegg' or 'tab' with this option.")
parser.add_option("-p", "--parseStyle",
default=KEGG,
choices=[ACCS,GIS,KEGG,HITID,HITDESC],
help="What should be parsed from the hit table: accessions('accs'), 'gis', K numbers in description ('kegg'), the full hit name('hitid'), or the full hit description('hitdesc'). (defaults to '%default')")
parser.add_option("-c", "--cutoff", dest="cutoff", type="float", default=0.01,
help="Cutoff for showing paths or genes. If a fractional count for a path/gene is below this value, it will be labelled None.",
metavar="CUTOFF")
# format and filterPct
addHitTableOptions(parser)
parser.add_option("-C", "--countMethod", dest="countMethod", default="all", choices=('first','most','all','consensus'),
help="How to deal with assignments from multiple hits. (first, most: can return multiple hits, all (default): return every hit, consensus: return None unless all the same)",
metavar="COUNTMETHOD")
parser.add_option("-r","--filterForKO",action="store_true", dest="koHitsOnly", default=False, help="ignore hits with no KO assignment. This means reads with no hits to KO tagged sequences will not be in the output.")
parser.add_option("-l","--level", dest="level", default="ko", choices=('ko','NAME','DEFINITION','EC','PATHWAY','1','2','3'), help="Either 'ko'; a string to look for in ko file ('PATHWAY','NAME', 'DEFINITION', or 'EC'); or level in kegg class heirarchy (1, 2, or 3 (should be same as PATHWAY))")
parser.add_option("-k", "--koFile", dest="ko", metavar="KOFILE", default=None,
help="File containing kegg heirarchy (either ko or ko00001.keg)")
addUniversalOptions(parser)
(options, args) = parser.parse_args()
setupLogging(options, description)
if options.infile is None:
infile = sys.stdin
else:
infile = open(options.infile)
if options.parseStyle==KEGG:
if options.mapFile is not None:
logging.warn("Do you REALLY want to apply a mapping to KOs?")
if options.level != 'ko':
if options.ko is None:
options.error("Please supply KEGG file if sepcifying a level other than 'ko' ")
# read KEGG file
koTranslation = readKEGGFile(options.ko, options.level)
else:
koTranslation = None
# map reads to hits
if options.mapFile is not None:
if options.mapStyle=='kegg' or ( options.mapStyle=='auto' and len(options.mapFile)>=13 and options.mapFile[-13:]=='genes_ko.list'):
valueMap=parseLinkFile(options.mapFile)
else:
if options.parseStyle == GIS:
keyType=int
else:
keyType=None
valueMap = parseMapFile(options.mapFile,valueType=None,keyType=keyType)
else:
valueMap=None
for (inhandle,outhandle) in inputIterator(args, options):
logging.debug("Reading from %s and writing to %s" % (inhandle, outhandle))
hitMap = parseM8File(inhandle, valueMap, options.hitTableFormat, options.filterTopPct, options.parseStyle, options.countMethod, ignoreEmptyHits=options.koHitsOnly,sortReads=options.hitTableSortReads)
# manipulate mappings
hitMap = applySimpleCutoff(hitMap, options.cutoff, koTranslation)
log("maps complete for %d reads" % (len(hitMap)))
# print out hit table
outhandle.write("Read\tHit\n")
if options.outputStyle=='python':
for read in sorted(hitMap.keys()):
hit=hitMap[read]
outhandle.write(str(read))
outhandle.write("\t")
outhandle.write(repr(hit))
outhandle.write("\n")
if options.outputStyle=='lines':
for read in sorted(hitMap.keys()):
hit=hitMap[read]
if type(hit) is type([]):
for h in sorted(hit):
outhandle.write(str(read))
outhandle.write("\t")
outhandle.write(str(h))
outhandle.write("\n")
else:
outhandle.write(str(read))
outhandle.write("\t")
outhandle.write(str(hit))
outhandle.write("\n")
else:
for read in sorted(hitMap.keys()):
hit=hitMap[read]
outhandle.write(str(read))
if type(hit) is type([]):
for h in sorted(hit):
outhandle.write("\t")
outhandle.write(str(h))
else:
outhandle.write("\t")
outhandle.write(str(hit))
outhandle.write("\n")