class UclustOTUs(OTUs):
"""Will use uclust via the qimme wraper to create OTU clusters from a given FASTA file
http://qiime.org/scripts/pick_otus.html"""
short_name = 'uclust'
title = 'UCLUST-QIIME denovo picking'
all_paths = """
/clusters/clusters.uc
/clusters/qiime.log
/clusters/all_otus.txt
/clusters/all_centers.fasta
/centers.fasta
/otus.txt
/taxonomy_silva/
/taxonomy_fw/
/graphs/
"""
def __repr__(self): return '<%s object of %s>' % (self.__class__.__name__, self.parent)
def __init__(self, cluster):
# Save parent #
self.cluster, self.parent = cluster, cluster
# Inherited #
self.samples = self.parent.samples
# Paths #
self.base_dir = self.parent.p.otus_dir + self.short_name + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Main FASTA file #
self.reads = self.parent.reads
# Files #
self.all_otus = FilePath(self.p.all_otus)
self.all_centers = FASTA(self.p.all_centers)
self.otus = FilePath(self.base_dir + "otus.txt")
self.centers = FASTA(self.base_dir + "centers.fasta")
# Taxonomy #
self.taxonomy_silva = CrestTaxonomy(self.centers, self, 'silvamod', self.p.silva)
self.taxonomy_fw = CrestTaxonomy(self.centers, self, 'freshwater', self.p.fw_dir)
# Preferred one #
self.taxonomy = self.taxonomy_silva
def run(self):
# Clean #
shutil.rmtree(self.p.clusters_dir)
# Run command #
pick_otus = sh.Command('pick_otus.py')
pick_otus('-m', 'uclust', '-i', self.reads, '-o', self.p.clusters_dir)
# Move into place #
base_name = self.p.clusters_dir + self.reads.prefix
shutil.move(base_name + '_otus.txt', self.all_otus)
shutil.move(base_name + '_otus.log', self.p.qiime_log)
shutil.move(base_name + '_clusters.uc', self.p.clusters_uc)
# Remove OTUs that are only one read #
def filter_singletons(f):
for line in f:
line = line.split()
if len(line) > 2: yield '\t'.join(line) + '\n'
self.otus.writelines(filter_singletons(self.all_otus))
# Create the centers file that is missing #
pick_rep = sh.Command('pick_rep_set.py')
pick_rep('-i', self.all_otus, '-f', self.reads, '-o', self.all_centers)
# Remake the centers file without the filtered OTUs #
self.otus_to_keep = [line.split()[0] for line in self.otus]
def filter_otus(f):
for seq in f:
if seq.id in self.otus_to_keep: yield seq
self.centers.write(filter_otus(self.all_centers))
@property_cached
def cluster_counts_table(self):
"""Create the unfiltered OTU table"""
# Put results in a dict of dicts #
result = defaultdict(lambda: defaultdict(int))
# Loop #
for line in self.otus:
# Parse the line #
contents = line.split()
otu, reads = contents[0], contents[1:]
# Parse the hits #
for r in reads:
nums = re.findall("run([0-9]+)_pool([0-9]+)_sample([0-9]+)_read([0-9]+)", r)
if nums:
run_num, pool_num, sample_num, read_num = map(int, nums[0])
sample = illumitag.runs[run_num][pool_num-1][sample_num-1]
name = sample.short_name
else:
nums = re.findall("run([0-9]+)_sample([0-9]+)_read([0-9]+)", r)
run_num, sample_num, read_num = map(int, nums[0])
sample = [s for s in illumitag.presamples+illumitag.pyrosamples if s.run_num==run_num and s.num==sample_num][0]
name = sample.short_name
# Count #
result[otu][name] += 1
# Return #
result = pandas.DataFrame(result)
result = result.fillna(0)
result = result.astype(int)
result = result.reindex_axis(sorted(result.columns, key=natural_sort), axis=1)
return result
