def run(self, threshold=3.0):
# Dereplicate #
sh.usearch7("--derep_fulllength", self.reads, '-output', self.derep, '-sizeout')
# Order by size and kill singeltons #
sh.usearch7("--sortbysize", self.derep, '-output', self.sorted, '-minsize', 2)
# Compute the centers #
sh.usearch7("--cluster_otus", self.sorted, '-otus', self.centers, '-otu_radius_pct', threshold)
# Rename the centers #
self.centers.rename_with_num('OTU_')
# Map the reads back to the centers #
identity = (100 - threshold) / 100
sh.usearch7("-usearch_global", self.reads, '-db', self.centers, '-strand', 'plus', '-id', identity, '-uc', self.readmap)
def run(self, threshold=None):
# Optional threshold #
if threshold is None: threshold = self.threshold
identity = (100 - threshold) / 100
# Dereplicate (uparse version 32bit version runs out of memory) #
if False: sh.usearch7("--derep_fulllength", self.reads, '-output', self.derep, '-sizeout')
sh.fasta_make_unique(self.reads, self.derep)
# Order by size and kill singeltons #
sh.usearch7("--sortbysize", self.derep, '-output', self.sorted, '-minsize', 2)
# Compute the centers #
sh.usearch7("--cluster_otus", self.sorted, '-otus', self.centers, '-otu_radius_pct', threshold)
# Rename the centers #
self.centers.rename_with_num('OTU-')
# Map the reads back to the centers #
sh.usearch7("-usearch_global", self.reads, '-db', self.centers, '-strand', 'plus', '-id', identity, '-uc', self.readmap)
# Internal modules #
import illumitag
from plumbing.common import natural_sort
from plumbing.autopaths import AutoPaths, FilePath
from plumbing.cache import property_cached, LazyString
from fasta import FASTA, SizesFASTA
from illumitag.clustering.otu import OTUs
from illumitag.clustering.taxonomy.crest import CrestTaxonomy
from illumitag.clustering.taxonomy.rdp import RdpTaxonomy
from illumitag.clustering.source.seqenv_wrapper import Seqenv
# Third party modules #
import sh, pandas
# Constants #
uparse_version = LazyString(lambda: sh.usearch7('-version').stdout[8:].strip('\n'))
###############################################################################
class UparseOTUs(OTUs):
"""Will use uparse to create OTU clusters from a given FASTA file
http://www.nature.com/doifinder/10.1038/nmeth.2604"""
short_name = 'uparse'
title = 'UPARSE denovo picking'
article = "http://www.nature.com/doifinder/10.1038/nmeth.2604"
version = uparse_version
threshold = 3.0
all_paths = """
/derep.fasta
/sorted.fasta