def __init__(self, path, parent):
# Save parent #
self.parent, self.pool = parent, parent
self.samples = parent.samples
# Auto paths #
self.base_dir = parent.p.quality_dir + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Files #
self.untrimmed = BarcodedFASTQ(path, samples=self.samples)
self.only_used = BarcodedFASTA(self.p.only_used, samples=self.samples)
self.trimmed = FASTA(self.p.trimmed)
# Qiime output #
self.qiime_fasta = FASTA(self.p.qiime_fasta)
# Mothur #
self.mothur_fasta = FASTA(self.p.mothur_fasta)
self.mothur_qual = QualFile(self.p.mothur_qual)
self.mothur_groups = FilePath(self.p.mothur_groups)
# Primer size #
self.trim_fwd = self.pool.samples.trim_fwd
self.trim_rev = self.pool.samples.trim_rev
class QualityReads(object):
"""A set of sequences determined to be quality controlled"""
all_paths = """
/mothur_reads.fasta
/mothur_reads.qual
/mothur_groups.tsv
/qiime_reads.fasta
/only_used_samples.fasta
/trimmed.fasta
"""
def __repr__(self): return '<%s object of %s>' % (self.__class__.__name__, self.parent)
def __len__(self): return len(self.trimmed)
def __init__(self, path, parent):
# Save parent #
self.parent, self.pool = parent, parent
self.samples = parent.samples
# Auto paths #
self.base_dir = parent.p.quality_dir + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Files #
self.untrimmed = BarcodedFASTQ(path, samples=self.samples)
self.only_used = BarcodedFASTA(self.p.only_used, samples=self.samples)
self.trimmed = FASTA(self.p.trimmed)
# Qiime output #
self.qiime_fasta = FASTA(self.p.qiime_fasta)
# Mothur #
self.mothur_fasta = FASTA(self.p.mothur_fasta)
self.mothur_qual = QualFile(self.p.mothur_qual)
self.mothur_groups = FilePath(self.p.mothur_groups)
# Primer size #
self.trim_fwd = self.pool.samples.trim_fwd
self.trim_rev = self.pool.samples.trim_rev
def filter_unused(self):
def no_unused_iterator(reads):
for r in reads.parse_barcodes():
if r.first.sample.used: yield r.read
self.only_used.write(no_unused_iterator(self.untrimmed))
def trim_primers(self):
def no_primers_iterator(reads):
for read in reads:
yield read[self.trim_fwd:-self.trim_rev]
self.trimmed.write(no_primers_iterator(self.only_used))
def make_mothur_output(self):
# Trimmed fasta #
self.mothur_fasta.link_from(self.trimmed.path)
# The groups file #
self.mothur_groups.create()
for r in self.only_used.parse_barcodes():
sample_name = r.first.sample.short_name
read_name = '%s\t%s\n' % (r.read.id, sample_name)
self.mothur_groups.handle.write(read_name)
self.mothur_groups.close()
def make_qiime_output(self):
# Prepare fasta writer #
handle = open(self.qiime_fasta.path, 'w')
writer = FastaWriter(handle, wrap=0)
writer.write_header()
# Counter #
counter = defaultdict(int)
# Do it #
for r in self.only_used.parse_barcodes():
sample_name = r.first.sample.short_name
counter[sample_name] += 1
r.read.id = '%s_%i %s' % (sample_name, counter[sample_name], r.read.id)
bar_seq = r.read.seq[0:self.pool.bar_len]
r.read.description = "orig_bc=%s new_bc=%s bc_diffs=0" % (bar_seq, bar_seq)
writer.write_record(r.read[self.trim_fwd:-self.trim_rev])
# Close #
writer.write_footer()
handle.close()