def test_sequence_stripper():
'It can cut using trimming recommendations'
seq1 = 'gggtctcatcatcaggg'.upper()
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1),
annotations={TRIMMING_RECOMMENDATIONS:{}})
trim_rec = seq.annotations[TRIMMING_RECOMMENDATIONS]
seq_trimmer = create_seq_trim_and_masker()
trim_rec['vector'] = [(0,3), (8, 12)]
seq2 = seq_trimmer(seq)
assert str(seq2.seq) == 'CTCA'
trim_rec['vector'] = [(0, 0), (8, 12)]
seq2 = seq_trimmer(seq)
assert str(seq2.seq) == 'GGTCTCA'
trim_rec['vector'] = [(0, 0), (8, 12)]
trim_rec['quality'] = []
trim_rec['mask'] = [(0, 3), (5, 6)]
seq2 = seq_trimmer(seq)
assert seq2.seq == 'ggtCtcA'
assert 'vector' not in trim_rec
assert 'quality' not in trim_rec
assert trim_rec['mask'] == [(0, 2), (4, 5)]
trim_rec['vector'] = [(0, 1), (8, 12)]
trim_rec['quality'] = [(1, 8), (13, 17)]
seq2 = seq_trimmer(seq)
assert seq2 is None
seq_trimmer = create_seq_trim_and_masker(mask=False)
trim_rec['vector'] = [(0, 0), (8, 12)]
trim_rec['quality'] = []
trim_rec['mask'] = [(0, 3), (5, 6)]
seq2 = seq_trimmer(seq)
assert seq2.seq == 'GGTCTCA'
assert seq2.annotations == {'trimming_recommendations':
{'mask': [(0, 2), (4, 5)]}}
seq_trimmer = create_seq_trim_and_masker()
seq3 = seq_trimmer(seq2)
assert seq3.seq == 'ggtCtcA'
#masking the regions to trim
seq_trimmer = create_seq_trim_and_masker(mask=True, trim_as_mask=True)
trim_rec['vector'] = [(0, 2), (8, 12)]
trim_rec['quality'] = []
trim_rec['mask'] = [(0, 1), (5, 6)]
seq2 = seq_trimmer(seq)
assert seq2.seq == 'gggTCtcAtcatcaggg'
assert seq2.annotations == {'trimming_recommendations':
{'mask': [(0, 1), (5, 6)]}}
def test_mask_low_complexity():
"It test mask_low_complexity function"
seq = "TCGCATCGATCATCGCAGATCGACTGATCGATCGATCGGGGGGGGGGGGGGGGGGGGGGGG"
seq = Seq(seq)
qual = [30] * 61
desc = "hola"
seq1 = SeqWithQuality(seq=seq, qual=qual, description=desc)
mask_low_complexity = create_masker_for_low_complexity()
masked_seq = mask_low_complexity(seq1)
sequence_trimmer = create_seq_trim_and_masker()
masked_seq = sequence_trimmer(masked_seq)
assert masked_seq.seq[-10:] == "gggggggggg"
assert len(masked_seq.qual) == 61
assert masked_seq.description == desc
seq = "GGGGGTTTCTTAAATTCGCCTGGAGATTTCATTCGGGGGGGGGGTTCTCCCCAGGGGGGGGTG"
seq += "GGGAAACCCCCCGTTTCCCCCCCCGCGCGCCTTTTCGGGGAAAATTTTTTTTTGTTCCCCCCG"
seq += "GAAAAAAAAATATTTCTCCTGCGGGGCCCCCGCGAAGAAAAAAGAAAAAAAAAAAGAGGAGGA"
seq += "GGGGGGGGGGGGCGAAAATATAGTTTGG"
seq1 = SeqWithQuality(seq=Seq(seq))
masked_seq = mask_low_complexity(seq1)
masked_seq = sequence_trimmer(masked_seq)
expected = "GGGGGTTTCTTAAATTCGCCTGGAGATTTCATtcggggggggggttctccccaggggg"
expected += "gggtggggAAaccccccgtttccccccccgcgcgccttttcggggaaaattttttttt"
expected += "gttccccccGGAAAAAAAAATATTTCTCCTGCGGGGCCCCCGCGaagaaaaaagaaaa"
expected += "aaaaaaaGAGGAGGAGGGgggggggggCGAAAATATAGTTTGG"
assert str(masked_seq.seq) == expected
def test_word_masker():
'It test if we remove words from the beginning of the seq'
word = 'ATAT'
seq1 = word + 'tctcatcatca'.upper()
seq1 = Seq(seq1)
seq = SeqWithQuality(seq1, qual=[30] * len(seq1))
remover = create_word_masker([word])
seq = remover(seq)
sequence_trimmer = create_seq_trim_and_masker()
seq = sequence_trimmer(seq)
assert seq.seq[0] == 'a'
seq1 = 'atactctcatcatca'.upper()
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
seq = remover(seq)
seq = sequence_trimmer(seq)
assert seq.seq == seq1
word = 'CA'
seq1 = 'ATCATCATCATCA'
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
remover = create_word_masker([word], False)
seq = remover(seq)
seq = sequence_trimmer(seq)
assert seq.seq == 'ATcaTcaTcaTca'
def test_word_masker():
"It test if we remove words from the beginning of the seq"
word = "ATAT"
seq1 = word + "tctcatcatca".upper()
seq1 = Seq(seq1)
seq = SeqWithQuality(seq1, qual=[30] * len(seq1))
remover = create_word_masker([word])
seq = remover(seq)
sequence_trimmer = create_seq_trim_and_masker()
seq = sequence_trimmer(seq)
assert seq.seq[0] == "a"
seq1 = "atactctcatcatca".upper()
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
seq = remover(seq)
seq = sequence_trimmer(seq)
assert seq.seq == seq1
word = "CA"
seq1 = "ATCATCATCATCA"
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
remover = create_word_masker([word], False)
seq = remover(seq)
seq = sequence_trimmer(seq)
assert seq.seq == "ATcaTcaTcaTca"
def test_mask_low_complexity():
'It test mask_low_complexity function'
seq = 'TCGCATCGATCATCGCAGATCGACTGATCGATCGATCGGGGGGGGGGGGGGGGGGGGGGGG'
seq = Seq(seq)
qual = [30] * 61
desc = 'hola'
seq1 = SeqWithQuality(seq=seq, qual=qual, description=desc)
mask_low_complexity = create_masker_for_low_complexity()
masked_seq = mask_low_complexity(seq1)
sequence_trimmer = create_seq_trim_and_masker()
masked_seq = sequence_trimmer(masked_seq)
assert masked_seq.seq[-10:] == 'gggggggggg'
assert len(masked_seq.qual) == 61
assert masked_seq.description == desc
seq = 'GGGGGTTTCTTAAATTCGCCTGGAGATTTCATTCGGGGGGGGGGTTCTCCCCAGGGGGGGGTG'
seq += 'GGGAAACCCCCCGTTTCCCCCCCCGCGCGCCTTTTCGGGGAAAATTTTTTTTTGTTCCCCCCG'
seq += 'GAAAAAAAAATATTTCTCCTGCGGGGCCCCCGCGAAGAAAAAAGAAAAAAAAAAAGAGGAGGA'
seq += 'GGGGGGGGGGGGCGAAAATATAGTTTGG'
seq1 = SeqWithQuality(seq=Seq(seq))
masked_seq = mask_low_complexity(seq1)
masked_seq = sequence_trimmer(masked_seq)
expected = 'GGGGGTTTCTTAAATTCGCCTGGAGATTTCATtcggggggggggttctccccaggggg'
expected += 'gggtggggAAaccccccgtttccccccccgcgcgccttttcggggaaaattttttttt'
expected += 'gttccccccGGAAAAAAAAATATTTCTCCTGCGGGGCCCCCGCGaagaaaaaagaaaa'
expected += 'aaaaaaaGAGGAGGAGGGgggggggggCGAAAATATAGTTTGG'
assert str(masked_seq.seq) == expected
def test_strip_seq_by_quality_lucy():
"It tests strip_seq_by_quality_lucy2"
seq = "ATCGATCAGTCAGACTGACAGACTCAGATCAGATCAGCATCAGCATACGATACGCATCAGACT"
seq += "ACGATCGATCGATCGACAGATCATCGATCATCGACGACTAGACGATCATCGATACGCAGACTC"
seq += "AGCAGACTACGAGATCAGCAGCATCAGCAGCA"
qual = "00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 "
qual += "00 00 00 00 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 "
qual += "60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 "
qual += "60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 "
qual += "60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 "
qual += "60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 "
qual += "60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 "
qual += "60 60 60 60 60 60 60 60 60 60 60 60 60 60 00 00 00 00"
qual = qual.split()
seq = Seq(seq)
seqrec1 = SeqWithQuality(name="seq1", seq=seq, qual=qual, description="desc1")
qual = "40 40 40 37 40 40 37 37 37 37 37 37 37 37 40 42 42 42 44 44 "
qual += "56 56 42 40 40 40 40 36 36 28 35 32 35 35 40 42 37 37 35 37 "
qual += "32 35 35 35 35 35 35 38 33 33 24 33 33 42 33 35 35 35 35 33 "
qual += "36 30 30 24 29 29 35 35 35 35 29 29 29 35 38 38 38 37 35 33 "
qual += "29 35 35 34 30 30 30 33 29 31 31 29 29 29 28 28 24 21 16 16 "
qual += "21 24 29 29 32 40 27 27 25 25 21 30 27 28 28 32 23 23 21 24 "
qual += "24 17 18 19 21 15 19 11 9 9 11 23 17 15 10 10 10 20 27 25 23 "
qual += "18 22 23 24 18 10 10 13 13 18 19 10 12 12 18 16 14 10 10 11 "
qual += "16 13 21 19 31 19 27 27 28 26 29 25 25 20 19 23 28 28 19 20 "
qual += "13 9 9 9 9 9 17 15 21 17 14 12 21 17 19 24 28 24 23 "
quality = qual.split()
seq = "ATCGATCAGTCAGACTGACAGACTCAGATCAGATCAGCATCAGCATACGATACGCATCAGACT"
seq += "ACGATCGATCGATCGACAGATCATCGATCATCGACGACTAGACGATCATCGATACGCAGACTC"
seq += "AGCAGACTACGAGATCAGCAGCATCAGCAGCAAGCAGACTACGAGATCAGCAGCATCAGCAGC"
seq += "ATTACGATGAT"
seq = Seq(seq)
seqrec2 = SeqWithQuality(seq=seq, qual=quality, name="seq2", description="desc2")
seq_iter = iter([seqrec1, seqrec2])
seq_trimmer = create_seq_trim_and_masker()
lucy_striper = create_striper_by_quality_lucy()
# pylint:disable-msg=W0612
seq_iter = lucy_striper(seq_iter)
new_seqs = []
for seq in seq_iter:
new_seqs.append(seq_trimmer(seq))
seq = new_seqs[0].seq
assert seqrec1.description == new_seqs[0].description
assert seq.startswith("CAGATCAGATCAGCATCAGCAT")
assert seq.endswith("CGAGATCAGCAGCATCAGC")
assert len(new_seqs) == 2
assert new_seqs[1].description == "desc2"
# now we test the sequence with adaptors
vector_fpath = os.path.join(TEST_DATA_DIR, "lucy", "icugi_vector.fasta")
splice_fpath = os.path.join(TEST_DATA_DIR, "lucy", "icugi_splice.fasta")
parameters = {"vector": [vector_fpath, splice_fpath], "bracket": [10, 0.02]}
lucy_striper = create_striper_by_quality_lucy(parameters)
seq_fhand = open(os.path.join(TEST_DATA_DIR, "lucy", "seq_with_adaptor1.fastq"))
seq_iter = lucy_striper(seqs_in_file(seq_fhand, format="fastq"))
new_seqs = []
for seq in seq_iter:
new_seqs.append(seq_trimmer(seq))
def test_trim_seq_by_qual_trimpoly(self):
"It test trimpoly but with trim low quality parameters"
seq = "ATCGATCTGATCTAGTCGATGTCTAGCTGAGCTACATAGCTAACGATCTAGTCTAGTCTATG"
seq += "TCATGTCATGTCGATGTCTAGTCTAGTCTAGTGAGTCACTGACTAGATCATGACATCGANNN"
seq += "NNNNNNNNNNNNNNNNNNTACTAGTC"
seq = Seq(seq)
qual = [10] * 150
desc = "hola"
seq1 = SeqWithQuality(seq=seq, qual=qual, description=desc)
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
sequence_trimmer = create_seq_trim_and_masker()
trimmed_seq = sequence_trimmer(trimmed_seq)
# It does not mask anything with this example, but it check that
# if works
assert trimmed_seq.seq.endswith("ATGACATCGA")
# another seq with the problem at the begining
seq = "TNNNNNNAGGGCTTTCCTGACAGCTANNNNNTTTGCGGGCAACATCCAGAACAAGCACCG"
seq += "GCAGATTGGCAATGCCGTGCCCCCGCCTCTTGCCTATGCACTTGGGAGGAAGCTGAAGGA"
seq += "AGCCGTTGACAAGCGTCAGGAAGCCAGCGCAGGCGTGCCTGCACCATGAGAAGTTTTCCT"
seq = Seq(seq)
seq1 = SeqWithQuality(seq=seq)
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
trimmed_seq = sequence_trimmer(trimmed_seq)
str_seq = str(trimmed_seq.seq)
assert str_seq.startswith("TTTGCGGGCAACA")
assert str_seq.endswith("GAGAAGTTTTCCT")
seq = "TGACATCGAACCTCGGCGCCGAGCACCTCCTCGCTGGGATGGTGGGCAAGAACTCCATGA"
seq += "AGGTCGCTCGCGATCTGGTCATGCAGGAGGTGAGGAGGCACTTCCGCCCTGAGCTGCTGA"
seq += "ACCGTCTCGACGAGATCGTGATCTTCGATCCTCTGTCCCACGAGCAGCTGAGGAAGGTCG"
seq += "CTCGCCTTCAGATGAAGGATGTGGCCGTCCGTCTTGCCGAANNNNNCATCGCTCTGGCTG"
seq += "TGACCGANNNNNCATTGGACATCATCTTGTCTCTCTCTNNNNNNTCNNNNT"
seq1 = SeqWithQuality(seq=Seq(seq))
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
trimmed_seq = sequence_trimmer(trimmed_seq)
str_seq = str(trimmed_seq.seq)
assert str_seq.startswith("TGACATCGAA")
assert str_seq.endswith("TCTTGCCGAA")
seq = "TACGGCCGGGGTNNCNNANNNNGCATTCTCGCAGGGTCTTTCTACACTATTAGATAAGAT"
seq += "GGATCCTTCTCAGAGAGTGAAGTTTGTTCAGGAAGTCAAGAAGGTTCTTGGATGATGATA"
seq += "TGATACCAACACATCCAACACAATATGCGCATGCTACATGTTATTTTTCAAGTACATACA"
seq += "TAGAAGGATATTGCTTGGCCTTGATTGATCATGTCTGATCTAAGTCGATCATTATTTTCT"
seq += "TGAAACTTCCTTTCGGACGTGGTGCTATGGTTGATGAATTTGGATGTGTGCGTTCTGCCA"
seq += "GGTGTAAGCCCAAAGGTTTATACAGACCGAGTTAAGGTTAGGAAGAGCACGAGTGAACTT"
seq1 = SeqWithQuality(seq=Seq(seq))
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
trimmed_seq = sequence_trimmer(trimmed_seq)
str_seq = str(trimmed_seq.seq)
assert str_seq.startswith("GCATTCTCGCAG")
assert str_seq.endswith("GTGAACTT")
def test_trim_seq_by_qual_trimpoly(self):
'It test trimpoly but with trim low quality parameters'
seq = 'ATCGATCTGATCTAGTCGATGTCTAGCTGAGCTACATAGCTAACGATCTAGTCTAGTCTATG'
seq += 'TCATGTCATGTCGATGTCTAGTCTAGTCTAGTGAGTCACTGACTAGATCATGACATCGANNN'
seq += 'NNNNNNNNNNNNNNNNNNTACTAGTC'
seq = Seq(seq)
qual = [10] * 150
desc = 'hola'
seq1 = SeqWithQuality(seq=seq, qual=qual, description=desc)
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
sequence_trimmer = create_seq_trim_and_masker()
trimmed_seq = sequence_trimmer(trimmed_seq)
# It does not mask anything with this example, but it check that
# if works
assert trimmed_seq.seq.endswith('ATGACATCGA')
#another seq with the problem at the begining
seq = 'TNNNNNNAGGGCTTTCCTGACAGCTANNNNNTTTGCGGGCAACATCCAGAACAAGCACCG'
seq += 'GCAGATTGGCAATGCCGTGCCCCCGCCTCTTGCCTATGCACTTGGGAGGAAGCTGAAGGA'
seq += 'AGCCGTTGACAAGCGTCAGGAAGCCAGCGCAGGCGTGCCTGCACCATGAGAAGTTTTCCT'
seq = Seq(seq)
seq1 = SeqWithQuality(seq=seq)
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
trimmed_seq = sequence_trimmer(trimmed_seq)
str_seq = str(trimmed_seq.seq)
assert str_seq.startswith('TTTGCGGGCAACA')
assert str_seq.endswith('GAGAAGTTTTCCT')
seq = 'TGACATCGAACCTCGGCGCCGAGCACCTCCTCGCTGGGATGGTGGGCAAGAACTCCATGA'
seq += 'AGGTCGCTCGCGATCTGGTCATGCAGGAGGTGAGGAGGCACTTCCGCCCTGAGCTGCTGA'
seq += 'ACCGTCTCGACGAGATCGTGATCTTCGATCCTCTGTCCCACGAGCAGCTGAGGAAGGTCG'
seq += 'CTCGCCTTCAGATGAAGGATGTGGCCGTCCGTCTTGCCGAANNNNNCATCGCTCTGGCTG'
seq += 'TGACCGANNNNNCATTGGACATCATCTTGTCTCTCTCTNNNNNNTCNNNNT'
seq1 = SeqWithQuality(seq=Seq(seq))
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
trimmed_seq = sequence_trimmer(trimmed_seq)
str_seq = str(trimmed_seq.seq)
assert str_seq.startswith('TGACATCGAA')
assert str_seq.endswith('TCTTGCCGAA')
seq = 'TACGGCCGGGGTNNCNNANNNNGCATTCTCGCAGGGTCTTTCTACACTATTAGATAAGAT'
seq += 'GGATCCTTCTCAGAGAGTGAAGTTTGTTCAGGAAGTCAAGAAGGTTCTTGGATGATGATA'
seq += 'TGATACCAACACATCCAACACAATATGCGCATGCTACATGTTATTTTTCAAGTACATACA'
seq += 'TAGAAGGATATTGCTTGGCCTTGATTGATCATGTCTGATCTAAGTCGATCATTATTTTCT'
seq += 'TGAAACTTCCTTTCGGACGTGGTGCTATGGTTGATGAATTTGGATGTGTGCGTTCTGCCA'
seq += 'GGTGTAAGCCCAAAGGTTTATACAGACCGAGTTAAGGTTAGGAAGAGCACGAGTGAACTT'
seq1 = SeqWithQuality(seq=Seq(seq))
strip_seq_by_quality_trimpoly = create_striper_by_quality_trimpoly()
trimmed_seq = strip_seq_by_quality_trimpoly(seq1)
trimmed_seq = sequence_trimmer(trimmed_seq)
str_seq = str(trimmed_seq.seq)
assert str_seq.startswith('GCATTCTCGCAG')
assert str_seq.endswith('GTGAACTT')
def test_edge_stripper():
'It test if we remove edges of the seq'
seq1 = 'gggtctcatcatcaggg'
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
edge_stripperr = create_edge_stripper(left_length=3, right_length=3)
sequence_trimmer = create_seq_trim_and_masker()
seq = edge_stripperr(seq)
seq = sequence_trimmer(seq)
assert seq.seq == 'tctcatcatca'
def test_mask_polya():
"It test mask_polyA function"
seq = "TCGCATCGATCATCGCAGATCGACTGATCGATCGATCAAAAAAAAAAAAAAAAAAAAAAA"
seq = Seq(seq)
seq1 = SeqWithQuality(seq=seq, description="hola")
mask_polya = create_masker_for_polia()
masked_seq = mask_polya(seq1)
sequence_trimmer = create_seq_trim_and_masker()
masked_seq = sequence_trimmer(masked_seq)
exp_seq = "TCGCATCGATCATCGCAGATCGACTGATCGATCGATCaaaaaaaaaaaaaaaaaaaaaaa"
assert masked_seq.seq == exp_seq
assert masked_seq.description == "hola"
def test_strip_short_adaptors():
"It tests the short adaptor removal with J. Forment sequences"
seq = "CgCGTGTCTCTAgATAGGGACAGTAGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAG"
seq += "ATGACGAGGCATTTGGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTA"
seq = Seq(seq)
seq = SeqWithQuality(name="seq", seq=seq)
seq_trimmer = create_seq_trim_and_masker()
strip_adap = create_re_word_striper(words=["CGTGTCTCTA", "TATATATA"])
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq).startswith("gATAGGGACAGTAGGAATCTCGTTAATC")
# two words
# 000000000011111111112222222222333333333344444444
# 012345678901234567890123456789012345678901234567
seq = "CgCGTGTCTCTAgATAGGGACAGTAGGAATTTTTTTcCGTGTCTCTAc"
seq = SeqWithQuality(name="seq", seq=Seq(seq))
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq) == "gATAGGGACAGTAGGAATTTTTTTc"
# We don't want the first region even if it's the longest one
seq = "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCgCGTGTCTCTAgC"
seq = SeqWithQuality(name="seq", seq=Seq(seq))
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq) == "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCg"
# Everything works if the adaptors are at the beginning and ends
seq = "CGTGTCTCTAcccccccccccccccTATATATAggggggggggCGTGTCTCTA"
seq = SeqWithQuality(name="seq", seq=Seq(seq))
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq) == "ccccccccccccccc"
# It test if we remove words from the beginning of the seq
word = "ATAT"
seq2 = "tctcatcatca"
seq1 = word + seq2 + word
word = "^" + word
seq1 = Seq(seq1)
seq = SeqWithQuality(seq1, qual=[30] * len(seq1))
remover = create_re_word_striper([word])
seq = remover(seq)
seq = seq_trimmer(seq)
assert seq.seq == seq2
def test_strip_short_adaptors():
'It tests the short adaptor removal with J. Forment sequences'
seq = 'CgCGTGTCTCTAgATAGGGACAGTAGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAG'
seq += 'ATGACGAGGCATTTGGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTA'
seq = Seq(seq)
seq = SeqWithQuality(name='seq', seq=seq)
seq_trimmer = create_seq_trim_and_masker()
strip_adap = create_re_word_striper(words=['CGTGTCTCTA', 'TATATATA'])
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq).startswith('gATAGGGACAGTAGGAATCTCGTTAATC')
#two words
# 000000000011111111112222222222333333333344444444
# 012345678901234567890123456789012345678901234567
seq = 'CgCGTGTCTCTAgATAGGGACAGTAGGAATTTTTTTcCGTGTCTCTAc'
seq = SeqWithQuality(name='seq', seq=Seq(seq))
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq) == 'gATAGGGACAGTAGGAATTTTTTTc'
#We don't want the first region even if it's the longest one
seq = 'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCgCGTGTCTCTAgC'
seq = SeqWithQuality(name='seq', seq=Seq(seq))
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq) == 'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCg'
#Everything works if the adaptors are at the beginning and ends
seq = 'CGTGTCTCTAcccccccccccccccTATATATAggggggggggCGTGTCTCTA'
seq = SeqWithQuality(name='seq', seq=Seq(seq))
clean_seq = strip_adap(seq)
clean_seq = seq_trimmer(clean_seq)
assert str(clean_seq.seq) == 'ccccccccccccccc'
#It test if we remove words from the beginning of the seq
word = 'ATAT'
seq2 = 'tctcatcatca'
seq1 = word + seq2 + word
word = '^' + word
seq1 = Seq(seq1)
seq = SeqWithQuality(seq1, qual=[30] * len(seq1))
remover = create_re_word_striper([word])
seq = remover(seq)
seq = seq_trimmer(seq)
assert seq.seq == seq2
def test_strip_vector_align_blast():
"It tests strip_vector_by_alignment using blast and UniVec"
vector = os.path.join(TEST_DATA_DIR, "blast", "univec+")
vec1 = "CTCGGGCCGTCTCTTGGGCTTGATCGGCCTTCTTGCGCATCTCACGCGCTCCTGCGGCGGCC"
vec1 += "TGTAGGGCAGGCTCATACCCCTGCCGAACCGCTTTTGTCAGCCGGTCGGCCACGGCTTCCGG"
vec1 += "CGTCTCAACGCGCTTT"
seq1 = "ATGCATCAGATGCATGCATGACTACGACTACGATCAGCATCAGCGATCAGCATCGATACGATC"
seq = SeqWithQuality(name="seq", seq=Seq(seq1 + vec1))
seq_trimmer = create_seq_trim_and_masker()
strip_vector_by_alignment = create_vector_striper(vector, "blastn")
striped_seq = strip_vector_by_alignment(seq)
striped_seq = seq_trimmer(striped_seq)
striped_seq = str(striped_seq.seq)
assert seq1[4:14] in striped_seq
assert seq1[-14:-4] in striped_seq
assert vec1[4:14] not in striped_seq
assert vec1[-14:-4] not in striped_seq
def test_strip_vector_align_blast():
'It tests strip_vector_by_alignment using blast and UniVec'
vector = os.path.join(TEST_DATA_DIR, 'blast', 'univec+')
vec1 = 'CTCGGGCCGTCTCTTGGGCTTGATCGGCCTTCTTGCGCATCTCACGCGCTCCTGCGGCGGCC'
vec1 += 'TGTAGGGCAGGCTCATACCCCTGCCGAACCGCTTTTGTCAGCCGGTCGGCCACGGCTTCCGG'
vec1 += 'CGTCTCAACGCGCTTT'
seq1 = 'ATGCATCAGATGCATGCATGACTACGACTACGATCAGCATCAGCGATCAGCATCGATACGATC'
seq = SeqWithQuality(name='seq', seq=Seq(seq1+vec1))
seq_trimmer = create_seq_trim_and_masker()
strip_vector_by_alignment = create_vector_striper(vector, 'blastn')
striped_seq = strip_vector_by_alignment(seq)
striped_seq = seq_trimmer(striped_seq)
striped_seq = str(striped_seq.seq)
assert seq1[4:14] in striped_seq
assert seq1[-14:-4] in striped_seq
assert vec1[4:14] not in striped_seq
assert vec1[-14:-4] not in striped_seq
def test_edge_stripper():
"It test if we remove edges of the seq"
seq1 = "gggtctcatcatcaggg"
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
edge_stripperr = create_edge_stripper(left_length=3, right_length=3)
sequence_trimmer = create_seq_trim_and_masker()
seq = edge_stripperr(seq)
seq = sequence_trimmer(seq)
assert seq.seq == "tctcatcatca"
seq1 = "gggtctcatcatcaggg"
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
edge_stripper = create_edge_stripper(left_length=1, right_length=2)
seq = edge_stripper(seq)
seq = sequence_trimmer(seq)
assert seq.seq == "ggtctcatcatcag"
seq1 = "gggtctcatcatcaggg"
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1))
edge_stripper = create_edge_stripper(left_length=10, right_length=0)
seq = edge_stripper(seq)
seq = sequence_trimmer(seq)
assert seq.seq == "atcaggg"
def test_strip_seq_by_quality():
"test trim_seq_by_quality "
seq = "ataataataata"
qual = [0] * len(seq)
desc = "hola"
seq1 = SeqWithQuality(qual=qual, seq=Seq(seq), description=desc)
strip_seq_by_quality = create_striper_by_quality(quality_treshold=40, min_seq_length=2, min_quality_bases=3)
seq_trimmer = create_seq_trim_and_masker()
new_seq = strip_seq_by_quality(seq1)
new_seq = seq_trimmer(new_seq)
assert new_seq is None
qual = [20, 20, 20, 60, 60, 60, 60, 60, 20, 20, 20, 20]
seq = "ataataataata"
desc = "hola"
seq1 = SeqWithQuality(qual=qual, seq=Seq(seq), description=desc)
strip_seq_by_quality = create_striper_by_quality(quality_treshold=40, min_seq_length=2, min_quality_bases=3)
seq_trimmer = create_seq_trim_and_masker()
new_seq = strip_seq_by_quality(seq1)
new_seq = seq_trimmer(new_seq)
assert new_seq.seq == "ataat"
assert new_seq.description == desc
qual = [60, 60, 60, 60, 60, 60, 60]
seq = "ataataa"
new_seq = strip_seq_by_quality(SeqWithQuality(qual=qual, seq=Seq(seq)))
new_seq = seq_trimmer(new_seq)
assert new_seq.seq == "ataataa"
qual = [60, 60, 60, 60, 60, 60, 0]
seq = "ataataa"
new_seq = strip_seq_by_quality(SeqWithQuality(qual=qual, seq=Seq(seq)))
new_seq = seq_trimmer(new_seq)
assert new_seq.seq == "ataata"
assert new_seq.qual == [60, 60, 60, 60, 60, 60]
qual = [40, 18, 10, 40, 40, 5, 8, 30, 14, 3, 40, 40, 40, 11, 6, 5, 3, 20, 10, 12, 8, 5, 4, 7, 1]
seq = "atatatatagatagatagatagatg"
strip_seq_by_quality = create_striper_by_quality(
quality_treshold=20, min_seq_length=2, min_quality_bases=3, quality_window_width=2
)
new_seq = strip_seq_by_quality(SeqWithQuality(qual=qual, seq=Seq(seq)))
new_seq = seq_trimmer(new_seq)
assert new_seq.qual == [40, 18, 10, 40, 40, 5, 8, 30, 14, 3, 40, 40, 40, 11]
qual = [40, 40, 13, 11, 40, 9, 40, 4, 27, 38, 40, 4, 11, 40, 40, 10, 10, 21, 3, 40, 9, 9, 12, 10, 9]
seq = "atatatatatatatatatatatata"
strip_seq_by_quality = create_striper_by_quality(
quality_treshold=20, min_seq_length=2, min_quality_bases=3, quality_window_width=1
)
new_seq = strip_seq_by_quality(SeqWithQuality(qual=qual, seq=Seq(seq)))
new_seq = seq_trimmer(new_seq)
assert new_seq.qual == [40, 40, 13, 11, 40, 9, 40, 4, 27, 38, 40]
# remove only from 3'
qual = [
1,
1,
1,
1,
1,
1,
1,
4,
27,
38,
40,
4,
11,
40,
40,
40,
40,
40,
40,
40,
10,
10,
21,
3,
40,
9,
9,
12,
10,
9,
]
seq = "atatatatatatatataaaaaatatatata"
strip_seq_by_quality = create_striper_by_quality(
quality_treshold=20, min_seq_length=2, min_quality_bases=3, quality_window_width=1, only_3_end=True
)
new_seq = strip_seq_by_quality(SeqWithQuality(qual=qual, seq=Seq(seq)))
new_seq = seq_trimmer(new_seq)
qual = new_seq.qual
assert qual[0] == 1
assert len(qual) == 20
# some solid reads
reads = """@8_19_812_F3
NACGATACGCTATGGGGAATGGCGAAAAAAGGGAAGGGAACTCACAGGA
+
!>=:BB<:>:A<A+5@?=6BA%<>AB9?<@B=1@BB7='A5@A@;98-2
"""
reads_fhand = tempfile.NamedTemporaryFile()
reads_fhand.write(reads)
seq = list(seqs_in_file(reads_fhand, format="fastq"))[0]
new_seq = strip_seq_by_quality(seq)
new_seq = seq_trimmer(new_seq)
assert len(new_seq) == 46
def test_sequence_stripper():
"It can cut using trimming recommendations"
seq1 = "gggtctcatcatcaggg".upper()
seq = SeqWithQuality(Seq(seq1), qual=[30] * len(seq1), annotations={TRIMMING_RECOMMENDATIONS: {}})
trim_rec = seq.annotations[TRIMMING_RECOMMENDATIONS]
seq_trimmer = create_seq_trim_and_masker()
trim_rec["vector"] = [(0, 3), (8, 12)]
seq2 = seq_trimmer(seq)
assert str(seq2.seq) == "CTCA"
trim_rec["vector"] = [(0, 0), (8, 12)]
seq2 = seq_trimmer(seq)
assert str(seq2.seq) == "GGTCTCA"
trim_rec["vector"] = [(0, 0), (8, 12)]
trim_rec["quality"] = []
trim_rec["mask"] = [(0, 3), (5, 6)]
seq2 = seq_trimmer(seq)
assert seq2.seq == "ggtCtcA"
assert "vector" not in trim_rec
assert "quality" not in trim_rec
assert trim_rec["mask"] == [(0, 2), (4, 5)]
trim_rec["vector"] = [(0, 1), (8, 12)]
trim_rec["quality"] = [(1, 8), (13, 17)]
seq2 = seq_trimmer(seq)
assert seq2 is None
seq_trimmer = create_seq_trim_and_masker(mask=False)
trim_rec["vector"] = [(0, 0), (8, 12)]
trim_rec["quality"] = []
trim_rec["mask"] = [(0, 3), (5, 6)]
seq2 = seq_trimmer(seq)
assert seq2.seq == "GGTCTCA"
assert seq2.annotations == {"trimming_recommendations": {"mask": [(0, 2), (4, 5)]}}
seq_trimmer = create_seq_trim_and_masker()
seq3 = seq_trimmer(seq2)
assert seq3.seq == "ggtCtcA"
# masking the regions to trim
seq_trimmer = create_seq_trim_and_masker(mask=True, trim_as_mask=True)
trim_rec["vector"] = [(0, 2), (8, 12)]
trim_rec["quality"] = []
trim_rec["mask"] = [(0, 1), (5, 6)]
seq2 = seq_trimmer(seq)
assert seq2.seq == "gggTCtcAtcatcaggg"
assert seq2.annotations == {"trimming_recommendations": {"mask": [(0, 1), (5, 6)]}}
# keep 5segment = False
seq_trimmer = create_seq_trim_and_masker()
trim_rec["vector"] = [(3, 5)]
trim_rec["quality"] = []
trim_rec["mask"] = []
seq2 = seq_trimmer(seq)
assert seq2.seq == "CATCATCAGGG"
# keep 5segment = True
seq_trimmer = create_seq_trim_and_masker(keep_5segment=True)
trim_rec["vector"] = [(3, 5)]
trim_rec["quality"] = []
trim_rec["mask"] = []
seq2 = seq_trimmer(seq)
assert seq2.seq == "GGG"
# masking the regions to trim
seq_trimmer = create_seq_trim_and_masker(mask=True, trim_as_mask=True, keep_5segment=True)
trim_rec["vector"] = [(0, 2), (8, 12)]
trim_rec["quality"] = []
trim_rec["mask"] = [(0, 1), (5, 6)]
seq2 = seq_trimmer(seq)
assert seq2.seq == seq.seq.lower()
assert seq2.annotations == {"trimming_recommendations": {"mask": [(0, 1), (5, 6)]}}
seq_trimmer = create_seq_trim_and_masker(keep_5segment=True)
trim_rec["vector"] = [(0, 2), (8, 12)]
trim_rec["quality"] = []
trim_rec["mask"] = [(0, 1), (5, 6)]
assert None == seq_trimmer(seq)
def test_strip_seq_by_quality_lucy():
'It tests strip_seq_by_quality_lucy2'
seq = 'ATCGATCAGTCAGACTGACAGACTCAGATCAGATCAGCATCAGCATACGATACGCATCAGACT'
seq += 'ACGATCGATCGATCGACAGATCATCGATCATCGACGACTAGACGATCATCGATACGCAGACTC'
seq += 'AGCAGACTACGAGATCAGCAGCATCAGCAGCA'
qual = '00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 '
qual += '00 00 00 00 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 '
qual += '60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 '
qual += '60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 '
qual += '60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 '
qual += '60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 '
qual += '60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 60 '
qual += '60 60 60 60 60 60 60 60 60 60 60 60 60 60 00 00 00 00'
qual = qual.split()
seq = Seq(seq)
seqrec1 = SeqWithQuality(name='seq1', seq=seq, qual=qual,
description ='desc1')
qual = '40 40 40 37 40 40 37 37 37 37 37 37 37 37 40 42 42 42 44 44 '
qual += '56 56 42 40 40 40 40 36 36 28 35 32 35 35 40 42 37 37 35 37 '
qual += '32 35 35 35 35 35 35 38 33 33 24 33 33 42 33 35 35 35 35 33 '
qual += '36 30 30 24 29 29 35 35 35 35 29 29 29 35 38 38 38 37 35 33 '
qual += '29 35 35 34 30 30 30 33 29 31 31 29 29 29 28 28 24 21 16 16 '
qual += '21 24 29 29 32 40 27 27 25 25 21 30 27 28 28 32 23 23 21 24 '
qual += '24 17 18 19 21 15 19 11 9 9 11 23 17 15 10 10 10 20 27 25 23 '
qual += '18 22 23 24 18 10 10 13 13 18 19 10 12 12 18 16 14 10 10 11 '
qual += '16 13 21 19 31 19 27 27 28 26 29 25 25 20 19 23 28 28 19 20 '
qual += '13 9 9 9 9 9 17 15 21 17 14 12 21 17 19 24 28 24 23 '
quality = qual.split()
seq = 'ATCGATCAGTCAGACTGACAGACTCAGATCAGATCAGCATCAGCATACGATACGCATCAGACT'
seq += 'ACGATCGATCGATCGACAGATCATCGATCATCGACGACTAGACGATCATCGATACGCAGACTC'
seq += 'AGCAGACTACGAGATCAGCAGCATCAGCAGCAAGCAGACTACGAGATCAGCAGCATCAGCAGC'
seq += 'ATTACGATGAT'
seq = Seq(seq)
seqrec2 = SeqWithQuality(seq=seq, qual=quality, name='seq2',
description ='desc2')
seq_iter = iter([seqrec1, seqrec2])
seq_trimmer = create_seq_trim_and_masker()
lucy_striper = create_striper_by_quality_lucy()
#pylint:disable-msg=W0612
seq_iter = lucy_striper(seq_iter)
new_seqs = []
for seq in seq_iter:
new_seqs.append(seq_trimmer(seq))
seq = new_seqs[0].seq
assert seqrec1.description == new_seqs[0].description
assert seq.startswith('CAGATCAGATCAGCATCAGCAT')
assert seq.endswith('CGAGATCAGCAGCATCAGC')
assert len(new_seqs) == 2
assert new_seqs[1].description == 'desc2'
# now we test the sequence with adaptors
vector_fpath = os.path.join(TEST_DATA_DIR, 'lucy', 'icugi_vector.fasta')
splice_fpath = os.path.join(TEST_DATA_DIR, 'lucy', 'icugi_splice.fasta')
parameters = {'vector':[vector_fpath, splice_fpath],
'bracket':[10, 0.02]}
lucy_striper = create_striper_by_quality_lucy(parameters)
seq_fhand = open(os.path.join(TEST_DATA_DIR, 'lucy',
'seq_with_adaptor1.fastq'))
seq_iter = lucy_striper(seqs_in_file(seq_fhand, format='fastq'))
new_seqs = []
for seq in seq_iter:
new_seqs.append(seq_trimmer(seq))
def test_strip_adaptor_blast(self):
"It tests strip_vector_by_alignment with blastn-short"
vec1 = SeqWithQuality(name="vec1", seq=Seq("atcgatcgatagcatacgat"))
vec2 = SeqWithQuality(name="vec2", seq=Seq("atgcatcagatcgataaaga"))
fhand_vectors = temp_fasta_file([vec1, vec2])
seq_trimmer = create_seq_trim_and_masker()
strip_vector_by_alignment = create_adaptor_striper(fhand_vectors)
seq = "ATGCATCAGATGCATGCATGACTACGACTACGATCAGCATCAGCGATCAGCATCGATACGATC"
seq = Seq(seq)
seq2 = SeqWithQuality(name="seq1", seq=seq)
seq1 = SeqWithQuality(name=seq2.name, seq=vec1.seq + seq2.seq + vec2.seq, description="hola")
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
assert seq3.description == "hola"
fhand_vectors.seek(0)
seq1 = SeqWithQuality(name=seq2.name, seq=vec1.seq + vec2.seq + seq2.seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
# overlaping vectors
fhand_vectors.seek(0)
new_seq = vec1.seq[:-2] + vec2.seq + seq2.seq + vec2.seq
seq1 = SeqWithQuality(name=seq2.name, seq=new_seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
# Now only vectors
fhand_vectors.seek(0)
new_seq = vec1.seq + vec2.seq + vec2.seq
seq1 = SeqWithQuality(name=seq2.name, seq=new_seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert seq3 is None
# Now without vectors
fhand_vectors.seek(0)
seq1 = seq2
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
fhand_vectors.seek(0)
seq1 = SeqWithQuality(name=seq2.name, seq=vec1.seq[::-1] + vec2.seq + seq2.seq)
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
seq = "ATGCATCAGATGCATGCATGACTACGACTACGATCAGCATCAGCGATCAGCATCGATACGATC"
seq = Seq(seq)
seq2 = SeqWithQuality(name="seq1", seq=seq)
# 'atcgatcgatagcatacgat atgcatcagatcgataaaga
seq = "atcgatcgatagcataGgat" + seq2.seq + "atgGatcagatcgataaaga"
seq1 = SeqWithQuality(name=seq2.name, seq=seq, description="hola")
seq3 = strip_vector_by_alignment(seq1)
seq3 = seq_trimmer(seq3)
assert str(seq2.seq) == str(seq3.seq)
long_adap = "atcgatcgatagcatacgatatcgatcgatagcatacgatatcgatcgatagcatacc"
vec1 = SeqWithQuality(name="vec1", seq=Seq(long_adap))
fhand_vectors = temp_fasta_file([vec1])
try:
create_adaptor_striper(fhand_vectors)
self.fail("ValueError expected")
except ValueError:
pass
