def truncate_rev_primers(fasta_f,
output_fp,
reverse_primers,
truncate_option='truncate_only',
primer_mismatches=2):
""" Locally aligns reverse primers, trucates or removes seqs
fasta_f: open file of fasta file
output_fp: open filepath to write truncated fasta to
reverse_primers: dictionary of SampleID:reverse primer sequence
truncate_option: either truncate_only, truncate_remove
primer_mismatches: number of allowed primer mismatches
"""
log_data = {
'sample_id_not_found':0,
'reverse_primer_not_found':0,
'total_seqs':0,
'seqs_written':0
}
for label, seq in MinimalFastaParser(fasta_f):
curr_label = label.split('_')[0]
log_data['total_seqs'] += 1
# Check fasta label for valid SampleID, if not found, just write seq
try:
curr_rev_primer = reverse_primers[curr_label]
except KeyError:
log_data['sample_id_not_found'] += 1
output_fp.write('>%s\n%s\n' % (label, seq))
log_data['seqs_written'] += 1
continue
mm_tests = {}
for rev_primer in curr_rev_primer:
rev_primer_mm, rev_primer_index =\
local_align_primer_seq(rev_primer, seq)
mm_tests[rev_primer_mm] = rev_primer_index
rev_primer_mm = min(mm_tests.keys())
rev_primer_index = mm_tests[rev_primer_mm]
if rev_primer_mm > primer_mismatches:
if truncate_option == "truncate_remove":
log_data['reverse_primer_not_found'] += 1
else:
log_data['reverse_primer_not_found'] += 1
log_data['seqs_written'] += 1
output_fp.write('>%s\n%s\n' % (label, seq))
else:
# Check for zero seq length after truncation, will not write seq
if rev_primer_index > 0:
log_data['seqs_written'] += 1
output_fp.write('>%s\n%s\n' % (label, seq[0:rev_primer_index]))
return log_data
def truncate_rev_primers(fasta_f,
output_fp,
reverse_primers,
truncate_option='truncate_only',
primer_mismatches=2):
""" Locally aligns reverse primers, trucates or removes seqs
fasta_f: open file of fasta file
output_fp: open filepath to write truncated fasta to
reverse_primers: dictionary of SampleID:reverse primer sequence
truncate_option: either truncate_only, truncate_remove
primer_mismatches: number of allowed primer mismatches
"""
log_data = {
'sample_id_not_found': 0,
'reverse_primer_not_found': 0,
'total_seqs': 0,
'seqs_written': 0
}
for label, seq in parse_fasta(fasta_f):
curr_label = label.split('_')[0]
log_data['total_seqs'] += 1
# Check fasta label for valid SampleID, if not found, just write seq
try:
curr_rev_primer = reverse_primers[curr_label]
except KeyError:
log_data['sample_id_not_found'] += 1
output_fp.write('>%s\n%s\n' % (label, seq))
log_data['seqs_written'] += 1
continue
mm_tests = {}
for rev_primer in curr_rev_primer:
rev_primer_mm, rev_primer_index =\
local_align_primer_seq(rev_primer, seq)
mm_tests[rev_primer_mm] = rev_primer_index
rev_primer_mm = min(mm_tests.keys())
rev_primer_index = mm_tests[rev_primer_mm]
if rev_primer_mm > primer_mismatches:
if truncate_option == "truncate_remove":
log_data['reverse_primer_not_found'] += 1
else:
log_data['reverse_primer_not_found'] += 1
log_data['seqs_written'] += 1
output_fp.write('>%s\n%s\n' % (label, seq))
else:
# Check for zero seq length after truncation, will not write seq
if rev_primer_index > 0:
log_data['seqs_written'] += 1
output_fp.write('>%s\n%s\n' % (label, seq[0:rev_primer_index]))
return log_data
def strip_primer(seqs, primer, maxmismatch=0, keep_primer=False):
'''strips 3 prime primer from sequences in fasta file and returns MinimalFastaParser
formatted arrays for stripped and not stripped sequences'''
nostripped = []
stripped = []
pri = primer.upper()
for head, seq in seqs:
RNA = False
seq = seq.upper()
if 'U' in seq:
seq = seq.replace('U', 'T')
RNA = True
#code adapted from truncate_reverse_primers.py in qiime
rev_primer_mm, rev_primer_index =\
local_align_primer_seq(pri, seq)
if rev_primer_mm > maxmismatch:
nostripped.append((head, seq))
continue
if keep_primer:
seqnew = seq[:rev_primer_index + len(primer)]
else:
seqnew = seq[:rev_primer_index]
if RNA:
seqnew = seqnew.replace('T', 'U')
stripped.append((head, seqnew))
#end for
return stripped, nostripped
