def parseM8FileIter(
inhandle,
hitStringMap,
format,
scorePct,
parsingStyle,
countMethod,
taxonomy=None,
rank=None,
ignoreEmptyHits=True,
sortReads=False):
"""
Wrapper method that combines filterM8, parseHits, and process hits to:
filter hits using format and scorePct
map reads to hits using parseHits
translate hits using processHits
If taxonomy is not None, hits will be TaxNode objects
contMethod can only be LCA if taxonomy given
Return an iterator over (read,hits) tuples.
"""
# check filtering options
if countMethod == 'first':
scorePct = -1
# get map from reads to lists of hit strings
logger.info("Parsing hits")
options = FilterParams()
options.format = format
if scorePct >= 0 or sortReads:
# filter hits on score if requested
if scorePct >= 0:
logger.info(
"Filtering for scores within %s pct of best" %
scorePct)
options.topPct = scorePct
options.sort = 'score'
options.sortReads = sortReads
# filters and parses
options.parseStyle = parsingStyle
hitIter = filterM8Stream(inhandle, options, returnLines=False)
# apply org or acc translation
# apply map of hit names if given'
# look up taxon node
hitIter = processHits(
hitIter,
hitStringMap=hitStringMap,
parseStyle=parsingStyle,
taxonomy=taxonomy,
rank=rank)
# apply count method
hitIter = applyCountMethod(hitIter, countMethod, ignoreEmptyHits)
return hitIter
def parseM8FileIter(inhandle, hitStringMap, format, scorePct, parsingStyle, countMethod, taxonomy=None, rank=None, ignoreEmptyHits=True, sortReads=False):
"""
Wrapper method that combines filterM8, parseHits, and process hits to:
filter hits using format and scorePct
map reads to hits using parseHits
translate hits using processHits
If taxonomy is not None, hits will be TaxNode objects
contMethod can only be LCA if taxonomy given
Return an iterator over (read,hits) tuples.
"""
# check filtering options
if countMethod == 'first':
scorePct=-1
# setup some variables
infoInDescription = parsingStyle in [KEGG,ORGS]
# get map from reads to lists of hit strings
logger.info("Parsing hits")
options=FilterParams()
options.format=format
if scorePct >= 0 or sortReads:
# filter hits on score if requested
if scorePct>=0:
logger.info("Filtering for scores within %s pct of best" % scorePct)
options.topPct=scorePct
options.sort='score'
options.sortReads=sortReads
# filters and parses
options.parseStyle=parsingStyle
hitIter=filterM8Stream(inhandle, options, returnLines=False)
# apply org or acc translation
# apply map of hit names if given'
# look up taxon node
hitIter = processHits(hitIter, hitStringMap=hitStringMap, parseStyle=parsingStyle, taxonomy=taxonomy, rank=rank)
#debugKey="F4UZ9WW02HMBZJ"
#logger.debug("Hits for %s: %r" % (debugKey,hitMap[debugKey]))
# apply count method
hitIter=applyCountMethod(hitIter, countMethod, ignoreEmptyHits)
return hitIter
