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# coding: utf-8
from __future__ import print_function, division, absolute_import
from cutadapt.colorspace import encode, decode
from cutadapt.scripts.cutadapt import main
from utils import run, datapath
# If there are any unknown characters in the test sequence,
# round tripping will only work if all characters after the
# first unknown character are also unknown:
# encode("TNGN") == "T444", but
# decode("T444") == "TNNN".
sequences = [
"",
"C",
"ACGGTC",
"TN",
"TN.",
"TNN.N",
"CCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTA",
"TGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGC",
"CAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGG"
]
def test_encode():
assert encode("AA") == "A0"
assert encode("AC") == "A1"
assert encode("AG") == "A2"
assert encode("AT") == "A3"
assert encode("CA") == "C1"
assert encode("CC") == "C0"
assert encode("CG") == "C3"
assert encode("CT") == "C2"
assert encode("GA") == "G2"
assert encode("GC") == "G3"
assert encode("GG") == "G0"
assert encode("GT") == "G1"
assert encode("TA") == "T3"
assert encode("TC") == "T2"
assert encode("TG") == "T1"
assert encode("TT") == "T0"
assert encode("TN") == "T4"
assert encode("NT") == "N4"
assert encode("NN") == "N4"
assert encode("ACGGTC") == "A13012"
assert encode("TTT.N") == "T0044"
assert encode("TTNT.N") == "T04444"
def test_decode():
for s in sequences:
expected = s.replace('.', 'N')
encoded = encode(s)
assert decode(encoded) == expected
assert decode('A.') == 'AN'
assert decode('C.') == 'CN'
assert decode('G.') == 'GN'
assert decode('T.') == 'TN'
def test_qualtrim_csfastaqual():
'''-q with csfasta/qual files'''
run("-c -q 10", "solidqual.fastq", "solid.csfasta", 'solid.qual')
def test_E3M():
'''Read the E3M dataset'''
# not really colorspace, but a fasta/qual file pair
main(['-o', '/dev/null', datapath("E3M.fasta"), datapath("E3M.qual")])
def test_bwa():
'''MAQ-/BWA-compatible output'''
run("-c -e 0.12 -a 330201030313112312 -x 552: --maq", "solidmaq.fastq", "solid.csfasta", 'solid.qual')
def test_bfast():
'''BFAST-compatible output'''
run("-c -e 0.12 -a 330201030313112312 -x abc: --strip-f3", "solidbfast.fastq", "solid.csfasta", 'solid.qual')
def test_trim_095():
'''some reads properly trimmed since cutadapt 0.9.5'''
run("-c -e 0.122 -a 330201030313112312", "solid.fasta", "solid.fasta")
def test_solid():
run("-c -e 0.122 -a 330201030313112312", "solid.fastq", "solid.fastq")
def test_solid_basespace_adapter():
'''colorspace adapter given in basespace'''
run("-c -e 0.122 -a CGCCTTGGCCGTACAGCAG", "solid.fastq", "solid.fastq")
def test_solid5p():
'''test 5' colorspace adapter'''
# this is not a real adapter, just a random string
# in colorspace: C0302201212322332333
run("-c -e 0.1 --trim-primer -g CCGGAGGTCAGCTCGCTATA", "solid5p.fasta", "solid5p.fasta")
def test_solid5p_prefix_notrim():
'''test anchored 5' colorspace adapter, no primer trimming'''
run("-c -e 0.1 -g ^CCGGAGGTCAGCTCGCTATA", "solid5p-anchored.notrim.fasta", "solid5p.fasta")
def test_solid5p_prefix():
'''test anchored 5' colorspace adapter'''
run("-c -e 0.1 --trim-primer -g ^CCGGAGGTCAGCTCGCTATA", "solid5p-anchored.fasta", "solid5p.fasta")
def test_solid5p_fastq():
'''test 5' colorspace adapter'''
# this is not a real adapter, just a random string
# in colorspace: C0302201212322332333
run("-c -e 0.1 --trim-primer -g CCGGAGGTCAGCTCGCTATA", "solid5p.fastq", "solid5p.fastq")
def test_solid5p_prefix_notrim_fastq():
'''test anchored 5' colorspace adapter, no primer trimming'''
run("-c -e 0.1 -g ^CCGGAGGTCAGCTCGCTATA", "solid5p-anchored.notrim.fastq", "solid5p.fastq")
def test_solid5p_prefix_fastq():
'''test anchored 5' colorspace adapter'''
run("-c -e 0.1 --trim-primer -g ^CCGGAGGTCAGCTCGCTATA", "solid5p-anchored.fastq", "solid5p.fastq")
def test_sra_fastq():
'''test SRA-formatted colorspace FASTQ'''
run("-c -e 0.1 --format sra-fastq -a CGCCTTGGCCGTACAGCAG", "sra.fastq", "sra.fastq")
def test_no_zero_cap():
run("--no-zero-cap -c -e 0.122 -a CGCCTTGGCCGTACAGCAG", "solid-no-zerocap.fastq", "solid.fastq")
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