def main():
description = __doc__
parser = argparse.ArgumentParser(description=description)
parser.add_argument("input_files", nargs="+",
default=[],
metavar="INFILE",
help="List of hit tables to process")
parser.add_argument("-o", "--outfile", dest="output_file",
metavar="OUTFILE", help="Write count table to OUTFILE")
parser.add_argument("-l", "--level", dest="levels", default=None,
metavar="LEVEL", action="append",
help=""" Level(s) to collect counts on. Use flag
multiple times to specify multiple levels. If multiple
values given, one table produced for each with rank
name appended to file name. Levels can be an integer
(1-3) for KEGG or SEED levels, any one of 'gene',
'role', 'family',
'ko', or 'ortholog' (which are all synonyms), or
anything not synonymous with 'gene' to
get CAZy groups. Defaults to ortholog/role and
levels 1, 2, and 3 for KEGG and SEED
and gene and group for CAZy and COG.""")
# option for deconvoluting clusters or assemblies
add_weight_arguments(parser, multiple=True)
# cutoff options
add_count_arguments(parser)
# format, ortholog heirarchy, and more
kegg.add_path_arguments(
parser,
defaults={'countMethod': 'tophit'},
choices={'countMethod':
('tophit',
'first',
'most',
'all',
'consensus')},
helps={'countMethod':
("How to deal with counts from multiple hits. ('first': "
"just use the first hit, 'most': "
"can return multiple hits, 'all': return every hit, "
"consensus: return None unless all the same). Do not "
"use most or consensus with more than one level at a time. "
"Default is 'tophit': This breaks any ties by choosing "
"the most abundant hit based on other unambiguous "
"assignments.")})
# log level and help
add_universal_arguments(parser)
arguments = parser.parse_args()
setup_logging(arguments)
if len(arguments.input_files) == 0:
parser.error("Must supply at least one m8 file to parse")
# Set defaults and check for some conflicts
if arguments.levels is None and arguments.heirarchyFile is None:
# using hit names only
arguments.levels = [None]
else:
if arguments.heirarchyFile is None \
and arguments.heirarchyType != 'cazy':
logging.warning("Type: %s", arguments.heirarchyType)
parser.error("Cannot select levels without a heirarchy (ko) file")
if arguments.levels is None:
# set a default
if arguments.heirarchyType is 'kegg':
arguments.levels = ['ko', '1', '2', 'pathway']
if arguments.heirarchyType is 'seed':
arguments.levels = ['role', '1', '2', 'subsystem']
else:
arguments.levels = ['gene', 'group']
try:
# Make sure the rank lists make sense
arguments.levels = cleanLevels(arguments.levels)
except Exception as e:
parser.error(str(e))
# load weights file
sequenceWeights = loadSequenceWeights(arguments.weights)
# only print to stdout if there is a single level
if len(arguments.levels) > 1 and arguments.output_file is None:
parser.error("STDOUT only works if a single level is chosen!")
cutoff = arguments.cutoff
# map reads to hits
if arguments.mapFile is not None:
if arguments.mapStyle == 'auto':
with open(arguments.mapFile) as f:
firstLine = next(f)
while len(firstLine) == 0 or firstLine[0] == '#':
firstLine = next(f)
if koMapRE.search(firstLine):
arguments.mapStyle = 'kegg'
elif seedMapRE.search(firstLine):
arguments.mapStyle = 'seed'
elif tabMapRE.search(firstLine):
arguments.mapStyle = 'tab'
# elif cogMapRE.search(firstLine):
# arguments.mapStyle='cog'
else:
raise Exception(
"Cannot figure out map type from first line:\n%s" %
(firstLine))
logging.info("Map file seems to be: %s", arguments.mapStyle)
if arguments.mapStyle == 'kegg':
valueMap = kegg.parseLinkFile(arguments.mapFile)
elif arguments.mapStyle == 'seed':
valueMap = kegg.parseSeedMap(arguments.mapFile)
# elif arguments.mapStyle=='cog':
# valueMap=kegg.parseCogMap(arguments.mapFile)
else:
if arguments.parseStyle == GIS:
keyType = int
else:
keyType = None
valueMap = parseMapFile(
arguments.mapFile,
valueType=None,
valueDelim=arguments.tab_map_delim,
keyType=keyType)
if len(valueMap) > 0:
logging.info("Read %d items into map. EG: %s",
len(valueMap), next(iter(valueMap.items())))
else:
logging.warn("Read 0 items into value map!")
else:
valueMap = None
# parse input files
fileCounts = {}
totals = {}
fileLabels = {}
sortedLabels = []
# Allow for file names to be preceded with TAG=
for filename in arguments.input_files:
bits = filename.split("=", 1)
if len(bits) > 1:
(filetag, filename) = bits
else:
filetag = filename
fileLabels[filename] = filetag
# keep order so that column order matches arguments
sortedLabels.append(filetag)
fileCounts[filetag] = {}
totals[filetag] = 0
params = FilterParams.create_from_arguments(arguments)
# TODO: incorporate weights into tophit algorithm!
if arguments.countMethod == 'tophit':
# Process all files at once and use overall abundance to pick best hits
from edl import redistribute
multifile = redistribute.multipleFileWrapper(fileLabels.items())
# don't give any hit translation, just use hit ids for redistribution
readHits = redistribute.pickBestHitByAbundance(
multifile,
filterParams=params,
returnLines=False,
winnerTakeAll=True,
parseStyle=arguments.parseStyle,
sequenceWeights=sequenceWeights)
# define method to turn Hits into Genes (kos, families)
hitTranslator = getHitTranslator(parseStyle=arguments.parseStyle,
hitStringMap=valueMap)
# translateHit = lambda hit: hitTranslator.translateHit(hit)[0]
# use read->file mapping and hit translator to get file based counts
# from returned (read,Hit) pairs
increment = 1
for (read_name, hit) in readHits:
file_tag, read_name = read_name.split("/", 1)
file_tag = unquote_plus(file_tag)
gene = hitTranslator.translateHit(hit)[0]
if gene is None:
gene = "None"
logging.debug(
"READ: %s\t%s\t%s\t%s",
file_tag, read_name, hit.hit, gene)
genecount = fileCounts[file_tag].setdefault(gene, 0)
if sequenceWeights is not None:
increment = sequenceWeights.get(read_name, 1)
fileCounts[file_tag][gene] = genecount + increment
totals[file_tag] += increment
logging.debug(str(totals))
else:
# Original way, just process each file separately
for (filename, filetag) in fileLabels.items():
infile = open(filename, 'rU')
hitIter = parseM8FileIter(infile,
valueMap,
params,
arguments.parseStyle,
arguments.countMethod,
ignoreEmptyHits=arguments.mappedHitsOnly)
(total, counts, hitMap) = \
countIterHits(hitIter,
allMethod=arguments.allMethod,
weights=sequenceWeights)
fileCounts[filetag] = counts
totals[filetag] = total
logging.info(
"parsed %d hits (%d unique) for %d reads from %s",
total, len(counts), len(hitMap), filename)
infile.close()
logging.debug(repr(fileCounts))
printCountTablesByLevel(fileCounts, totals, sortedLabels, arguments)
def main():
description = __doc__
parser = argparse.ArgumentParser(description)
add_IO_arguments(parser)
parser.add_argument("-l",
"--level",
dest="levels",
default=None,
metavar="LEVEL",
action="append",
help=""" Level(s) to collect counts on. Use flag
multiple times to specify multiple levels. If multiple
values given, one table produced for each with rank
name appended to file name. Levels can be an integer
(1-3) for KEGG or SEED levels, any one of 'gene',
'role', 'family',
'ko', or 'ortholog' (which are all synonyms), or
anything not synonymous with 'gene' to
get CAZy groups. Defaults to ortholog/role and
levels 1, 2, and 3 for KEGG and SEED
and gene and group for CAZy and COG.""")
parser.add_argument(
'-S',
'--squash',
dest='splitForLevels',
default=True,
action='store_false',
help="Don't split assignment rows if gene maps to multiple pathways, "
"just squash them into one row using python list syntax")
# format, ortholog heirarchy, and more
kegg.add_path_arguments(parser)
# log level and help
add_universal_arguments(parser)
arguments = parser.parse_args()
setup_logging(arguments)
# Set defaults and check for some conflicts
if arguments.levels is None and arguments.heirarchyFile is None:
# using hit names only
arguments.levels = [None]
else:
if arguments.heirarchyFile is None \
and arguments.heirarchyType != 'cazy':
logging.warn("Type: %s" % (arguments.heirarchyType))
parser.error("Cannot select levels without a heirarchy (ko) file")
if arguments.levels is None:
# set a default
if arguments.heirarchyType is 'kegg':
arguments.levels = ['ko', '1', '2', 'pathway']
if arguments.heirarchyType is 'seed':
arguments.levels = ['role', '1', '2', 'subsystem']
else:
arguments.levels = ['gene', 'group']
try:
# Make sure the level list makes sense
arguments.levels = cleanLevels(arguments.levels)
except Exception as e:
parser.error(str(e))
# map reads to hits
if arguments.mapFile is not None:
if arguments.mapStyle == 'auto':
with open(arguments.mapFile) as f:
firstLine = next(f)
while len(firstLine) == 0 or firstLine[0] == '#':
firstLine = next(f)
if koMapRE.search(firstLine):
arguments.mapStyle = 'kegg'
elif seedMapRE.search(firstLine):
arguments.mapStyle = 'seed'
elif tabMapRE.search(firstLine):
arguments.mapStyle = 'tab'
elif cogMapRE.search(firstLine):
arguments.mapStyle = 'cog'
else:
raise Exception(
"Cannot figure out map type from first line:\n%s" %
(firstLine))
logging.info("Map file seems to be: %s" % (arguments.mapStyle))
if arguments.mapStyle == 'kegg':
valueMap = kegg.parseLinkFile(arguments.mapFile)
elif arguments.mapStyle == 'seed':
valueMap = kegg.parseSeedMap(arguments.mapFile)
elif arguments.mapStyle == 'cog':
valueMap = kegg.parseCogMap(arguments.mapFile)
else:
if arguments.parseStyle == hits.GIS:
keyType = int
else:
keyType = None
valueMap = parseMapFile(arguments.mapFile,
valueType=None,
valueDelim=arguments.tab_map_delim,
keyType=keyType)
if len(valueMap) > 0:
logging.info("Read %d items into map. EG: %s" %
(len(valueMap), next(iter(valueMap.items()))))
else:
logging.warn("Read 0 items into value map!")
else:
valueMap = None
# set up level mapping
levelMappers = [getLevelMapper(lvl, arguments) for lvl in arguments.levels]
# parse input files
for (inhandle, outhandle) in inputIterator(arguments):
logging.debug("Reading from %s and writing to %s" %
(inhandle, outhandle))
hitMapIter = hits.parseM8FileIter(
inhandle,
valueMap,
hits.FilterParams.create_from_arguments(arguments),
arguments.parseStyle,
arguments.countMethod,
ignoreEmptyHits=arguments.mappedHitsOnly)
if arguments.levels == [None]:
arguments.levels = ['Hit']
outhandle.write("Read\t%s\n" % ('\t'.join(arguments.levels)))
for read, hitIter in hitMapIter:
assignments = []
for hit in hitIter:
logging.debug("Hit: %s" % (hit))
assignment = []
for levelMapper in levelMappers:
assignment.append(levelMapper(hit))
assignments.append(assignment)
logging.debug("Read %s has %d hits" % (read, len(assignments)))
for assignment in assignments:
for assignmentList in handleMultipleMappings(
assignment, arguments):
outhandle.write("%s\t%s\n" %
(read, "\t".join(assignmentList)))
def main():
description = __doc__
parser = argparse.ArgumentParser(description)
add_IO_arguments(parser)
parser.add_argument("-l", "--level", dest="levels", default=None,
metavar="LEVEL", action="append",
help=""" Level(s) to collect counts on. Use flag
multiple times to specify multiple levels. If multiple
values given, one table produced for each with rank
name appended to file name. Levels can be an integer
(1-3) for KEGG or SEED levels, any one of 'gene',
'role', 'family',
'ko', or 'ortholog' (which are all synonyms), or
anything not synonymous with 'gene' to
get CAZy groups. Defaults to ortholog/role and
levels 1, 2, and 3 for KEGG and SEED
and gene and group for CAZy and COG.""")
parser.add_argument(
'-s',
'--squash',
dest='splitForLevels',
default=True,
action='store_false',
help="Don't split assignment rows if gene maps to multiple pathways, "
"just squash them into one row using python list syntax")
# format, ortholog heirarchy, and more
kegg.add_path_arguments(parser)
# log level and help
add_universal_arguments(parser)
arguments = parser.parse_args()
setup_logging(arguments)
# Set defaults and check for some conflicts
if arguments.levels is None and arguments.heirarchyFile is None:
# using hit names only
arguments.levels = [None]
else:
if arguments.heirarchyFile is None \
and arguments.heirarchyType != 'cazy':
logging.warn("Type: %s" % (arguments.heirarchyType))
parser.error("Cannot select levels without a heirarchy (ko) file")
if arguments.levels is None:
# set a default
if arguments.heirarchyType is 'kegg':
arguments.levels = ['ko', '1', '2', 'pathway']
if arguments.heirarchyType is 'seed':
arguments.levels = ['role', '1', '2', 'subsystem']
else:
arguments.levels = ['gene', 'group']
try:
# Make sure the level list makes sense
arguments.levels = cleanLevels(arguments.levels)
except Exception as e:
parser.error(str(e))
# map reads to hits
if arguments.mapFile is not None:
if arguments.mapStyle == 'auto':
with open(arguments.mapFile) as f:
firstLine = next(f)
while len(firstLine) == 0 or firstLine[0] == '#':
firstLine = next(f)
if koMapRE.search(firstLine):
arguments.mapStyle = 'kegg'
elif seedMapRE.search(firstLine):
arguments.mapStyle = 'seed'
elif tabMapRE.search(firstLine):
arguments.mapStyle = 'tab'
elif cogMapRE.search(firstLine):
arguments.mapStyle = 'cog'
else:
raise Exception(
"Cannot figure out map type from first line:\n%s" %
(firstLine))
logging.info("Map file seems to be: %s" % (arguments.mapStyle))
if arguments.mapStyle == 'kegg':
valueMap = kegg.parseLinkFile(arguments.mapFile)
elif arguments.mapStyle == 'seed':
valueMap = kegg.parseSeedMap(arguments.mapFile)
elif arguments.mapStyle == 'cog':
valueMap = kegg.parseCogMap(arguments.mapFile)
else:
if arguments.parseStyle == hits.GIS:
keyType = int
else:
keyType = None
valueMap = parseMapFile(
arguments.mapFile,
valueType=None,
keyType=keyType)
if len(valueMap) > 0:
logging.info("Read %d items into map. EG: %s" %
(len(valueMap), next(iter(valueMap.items()))))
else:
logging.warn("Read 0 items into value map!")
else:
valueMap = None
# set up level mapping
levelMappers = [getLevelMapper(l, arguments) for l in arguments.levels]
# parse input files
for (inhandle, outhandle) in inputIterator(arguments):
logging.debug(
"Reading from %s and writing to %s" %
(inhandle, outhandle))
hitMapIter = hits.parseM8FileIter(
inhandle,
valueMap,
arguments.hitTableFormat,
arguments.filterTopPct,
arguments.parseStyle,
arguments.countMethod,
ignoreEmptyHits=arguments.mappedHitsOnly)
if arguments.levels == [None]:
arguments.levels = ['Hit']
outhandle.write("Read\t%s\n" % ('\t'.join(arguments.levels)))
for read, hitIter in hitMapIter:
assignments = []
for hit in hitIter:
logging.debug("Hit: %s" % (hit))
assignment = []
for levelMapper in levelMappers:
assignment.append(levelMapper(hit))
assignments.append(assignment)
logging.debug("Read %s has %d hits" % (read, len(assignments)))
for assignment in assignments:
for assignmentList in handleMultipleMappings(
assignment, arguments):
outhandle.write(
"%s\t%s\n" %
(read, "\t".join(assignmentList)))
def main():
description = __doc__
parser = argparse.ArgumentParser(description=description)
parser.add_argument("input_files",
nargs="+",
default=[],
metavar="INFILE",
help="List of hit tables to process")
parser.add_argument("-o",
"--outfile",
dest="output_file",
metavar="OUTFILE",
help="Write count table to OUTFILE")
parser.add_argument("-l",
"--level",
dest="levels",
default=None,
metavar="LEVEL",
action="append",
help=""" Level(s) to collect counts on. Use flag
multiple times to specify multiple levels. If multiple
values given, one table produced for each with rank
name appended to file name. Levels can be an integer
(1-3) for KEGG or SEED levels, any one of 'gene',
'role', 'family',
'ko', or 'ortholog' (which are all synonyms), or
anything not synonymous with 'gene' to
get CAZy groups. Defaults to ortholog/role and
levels 1, 2, and 3 for KEGG and SEED
and gene and group for CAZy and COG.""")
# option for deconvoluting clusters or assemblies
add_weight_arguments(parser, multiple=True)
# cutoff options
add_count_arguments(parser)
# format, ortholog heirarchy, and more
kegg.add_path_arguments(
parser,
defaults={'countMethod': 'tophit'},
choices={
'countMethod': ('tophit', 'first', 'most', 'all', 'consensus')
},
helps={
'countMethod':
("How to deal with counts from multiple hits. ('first': "
"just use the first hit, 'most': "
"can return multiple hits, 'all': return every hit, "
"consensus: return None unless all the same). Do not "
"use most or consensus with more than one level at a time. "
"Default is 'tophit': This breaks any ties by choosing "
"the most abundant hit based on other unambiguous "
"assignments.")
})
# log level and help
add_universal_arguments(parser)
arguments = parser.parse_args()
setup_logging(arguments)
if len(arguments.input_files) == 0:
parser.error("Must supply at least one m8 file to parse")
# Set defaults and check for some conflicts
if arguments.levels is None and arguments.heirarchyFile is None:
# using hit names only
arguments.levels = [None]
else:
if arguments.heirarchyFile is None \
and arguments.heirarchyType != 'cazy':
logging.warning("Type: %s", arguments.heirarchyType)
parser.error("Cannot select levels without a heirarchy (ko) file")
if arguments.levels is None:
# set a default
if arguments.heirarchyType is 'kegg':
arguments.levels = ['ko', '1', '2', 'pathway']
if arguments.heirarchyType is 'seed':
arguments.levels = ['role', '1', '2', 'subsystem']
else:
arguments.levels = ['gene', 'group']
try:
# Make sure the rank lists make sense
arguments.levels = cleanLevels(arguments.levels)
except Exception as e:
parser.error(str(e))
# load weights file
sequenceWeights = loadSequenceWeights(arguments.weights)
# only print to stdout if there is a single level
if len(arguments.levels) > 1 and arguments.output_file is None:
parser.error("STDOUT only works if a single level is chosen!")
cutoff = arguments.cutoff
# map reads to hits
if arguments.mapFile is not None:
if arguments.mapStyle == 'auto':
with open(arguments.mapFile) as f:
firstLine = next(f)
while len(firstLine) == 0 or firstLine[0] == '#':
firstLine = next(f)
if koMapRE.search(firstLine):
arguments.mapStyle = 'kegg'
elif seedMapRE.search(firstLine):
arguments.mapStyle = 'seed'
elif tabMapRE.search(firstLine):
arguments.mapStyle = 'tab'
# elif cogMapRE.search(firstLine):
# arguments.mapStyle='cog'
else:
raise Exception(
"Cannot figure out map type from first line:\n%s" %
(firstLine))
logging.info("Map file seems to be: %s", arguments.mapStyle)
if arguments.mapStyle == 'kegg':
valueMap = kegg.parseLinkFile(arguments.mapFile)
elif arguments.mapStyle == 'seed':
valueMap = kegg.parseSeedMap(arguments.mapFile)
# elif arguments.mapStyle=='cog':
# valueMap=kegg.parseCogMap(arguments.mapFile)
else:
if arguments.parseStyle == GIS:
keyType = int
else:
keyType = None
valueMap = parseMapFile(arguments.mapFile,
valueType=None,
valueDelim=arguments.tab_map_delim,
keyType=keyType)
if len(valueMap) > 0:
logging.info("Read %d items into map. EG: %s", len(valueMap),
next(iter(valueMap.items())))
else:
logging.warn("Read 0 items into value map!")
else:
valueMap = None
# parse input files
fileCounts = {}
totals = {}
fileLabels = {}
sortedLabels = []
# Allow for file names to be preceded with TAG=
for filename in arguments.input_files:
bits = filename.split("=", 1)
if len(bits) > 1:
(filetag, filename) = bits
else:
filetag = filename
fileLabels[filename] = filetag
# keep order so that column order matches arguments
sortedLabels.append(filetag)
fileCounts[filetag] = {}
totals[filetag] = 0
# TODO: incorporate weights into tophit algorithm!
if arguments.countMethod == 'tophit':
# Process all files at once and use overall abundance to pick best hits
from edl import redistribute
params = FilterParams.create_from_arguments(arguments)
multifile = redistribute.multipleFileWrapper(fileLabels.items())
# don't give any hit translation, just use hit ids for redistribution
readHits = redistribute.pickBestHitByAbundance(
multifile,
filterParams=params,
returnLines=False,
winnerTakeAll=True,
parseStyle=arguments.parseStyle,
sequenceWeights=sequenceWeights)
# define method to turn Hits into Genes (kos, families)
hitTranslator = getHitTranslator(parseStyle=arguments.parseStyle,
hitStringMap=valueMap)
# translateHit = lambda hit: hitTranslator.translateHit(hit)[0]
# use read->file mapping and hit translator to get file based counts
# from returned (read,Hit) pairs
increment = 1
for (read_name, hit) in readHits:
file_tag, read_name = read_name.split("/", 1)
file_tag = unquote_plus(file_tag)
gene = hitTranslator.translateHit(hit)[0]
if gene is None:
gene = "None"
logging.debug("READ: %s\t%s\t%s\t%s", file_tag, read_name, hit.hit,
gene)
genecount = fileCounts[file_tag].setdefault(gene, 0)
if sequenceWeights is not None:
increment = sequenceWeights.get(read_name, 1)
fileCounts[file_tag][gene] = genecount + increment
totals[file_tag] += increment
logging.debug(str(totals))
else:
# Original way, just process each file separately
for (filename, filetag) in fileLabels.items():
infile = open(filename, 'rU')
hitIter = parseM8FileIter(infile,
valueMap,
arguments.hitTableFormat,
arguments.filter_top_pct,
arguments.parseStyle,
arguments.countMethod,
ignoreEmptyHits=arguments.mappedHitsOnly)
(total, counts, hitMap) = \
countIterHits(hitIter,
allMethod=arguments.allMethod,
weights=sequenceWeights)
fileCounts[filetag] = counts
totals[filetag] = total
logging.info("parsed %d hits (%d unique) for %d reads from %s",
total, len(counts), len(hitMap), filename)
infile.close()
logging.debug(repr(fileCounts))
printCountTablesByLevel(fileCounts, totals, sortedLabels, arguments)
