def get_consensus(aligned_r1, aligned_r2):
consensus_seq = ctypes.create_string_buffer(aligned_r1.sequence)
consensus_qual = ctypes.create_string_buffer(aligned_r1.qualities)
for pos in range(len(aligned_r1)):
if aligned_r2.qualities[pos] > consensus_qual[pos]:
consensus_seq[pos] = aligned_r2.sequence[pos]
consensus_qual[pos] = aligned_r2.qualities[pos]
#Removes illumina's pair info from the consensus sequence name
consensus_obj = seqio.Sequence(
aligned_r1.name.split(" ")[0], consensus_seq.value,
consensus_qual.value)
return consensus_obj
def test_too_many_qualities():
seqio.Sequence(name="name", sequence="ACGT", qualities="#####")
def align_sequences(r1, r2):
new_r2 = seqio.Sequence(r2.name, rev_complement(r2.sequence),
r2.qualities[::-1])
return r1, new_r2
# coding: utf-8
from __future__ import print_function, division, absolute_import
import sys
from textwrap import dedent
from nose.tools import raises
from cutadapt import seqio
from cutadapt.compat import StringIO
# files tests/data/simple.fast{q,a}
simple_fastq = [
seqio.Sequence("first_sequence", "SEQUENCE1", ":6;;8<=:<"),
seqio.Sequence("second_sequence", "SEQUENCE2", "83<??:(61")
]
simple_fasta = [seqio.Sequence(x.name, x.sequence, None) for x in simple_fastq]
def test_fastareader():
with seqio.FastaReader("tests/data/simple.fasta") as f:
reads = list(f)
assert reads == simple_fasta
fasta = StringIO(
">first_sequence\nSEQUENCE1\n>second_sequence\nSEQUENCE2\n")
reads = list(seqio.FastaReader(fasta))
assert reads == simple_fasta
def test_fastareader_with_comments():
fasta = StringIO(