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"""
Tests for the sqt.io.fasta module
"""
from io import StringIO
import pytest
from sqt.io.fasta import (FastaReader, FastaWriter, Sequence, FastqWriter,
SequenceReader, fastq_header)
import os.path
def dpath(path):
return os.path.join(os.path.dirname(__file__), path)
def test_fastqwriter():
tmp = dpath("tmp.fastq")
with FastqWriter(tmp) as fq:
fq.write("name", "CCATA", "!#!#!")
fq.write("name2", "HELLO", "&&&!&&")
assert fq._file.closed
with open(tmp) as t:
assert t.read() == '@name\nCCATA\n+\n!#!#!\n@name2\nHELLO\n+\n&&&!&&\n'
os.remove(tmp)
def test_fastqwriter_twoheaders():
tmp = dpath("tmp.fastq")
with FastqWriter(tmp, twoheaders=True) as fq:
fq.write("name", "CCATA", "!#!#!")
fq.write("name2", "HELLO", "&&&!&&")
assert fq._file.closed
with open(tmp) as t:
assert t.read() == '@name\nCCATA\n+name\n!#!#!\n@name2\nHELLO\n+name2\n&&&!&&\n'
os.remove(tmp)
def test_fastawriter():
tmp = dpath("tmp.fasta")
with FastaWriter(tmp) as fw:
fw.write("name", "CCATA")
fw.write("name2", "HELLO")
assert fw._file.closed
with open(tmp) as t:
assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
os.remove(tmp)
def test_fastawriter_linelength():
tmp = dpath("tmp.fasta")
with FastaWriter(tmp, line_length=3) as fw:
fw.write("name", "CCAT")
fw.write("name2", "TACCAG")
assert fw._file.closed
with open(tmp) as t:
d = t.read()
assert d == '>name\nCCA\nT\n>name2\nTAC\nCAG\n'
os.remove(tmp)
def test_fastawriter_sequence():
tmp = dpath("tmp.fasta")
with FastaWriter(tmp) as fw:
fw.write(Sequence("name", "CCATA"))
fw.write(Sequence("name2", "HELLO"))
assert fw._file.closed
with open(tmp) as t:
assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
os.remove(tmp)
def test_fastawriter_contextmanager():
with pytest.raises(ValueError):
tmp = dpath("tmp.fasta")
fr = FastaWriter(tmp)
os.remove(tmp)
with fr as frw:
pass
with fr as frw:
pass
def test_fastareader():
with FastaReader(dpath("seq.fa"), case='keep') as fr:
seqs = list(fr)
assert fr._file.closed
assert len(seqs) == 3
assert seqs[0].qualities is None
assert seqs[0].name == 'Chr1'
assert seqs[1].name == 'Chr2 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02'
assert len(seqs[0].sequence) == 1235
assert seqs[0].sequence.startswith('CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATC')
assert seqs[1].sequence.startswith('ctcgaccaggacgatgaatgggc')
assert seqs[2].sequence.endswith('AATCTTGCAAGTTCCAACTAATT')
def test_fastareader_upper():
with FastaReader(dpath("seq.fa")) as fr:
seqs = list(fr)
assert seqs[0].name == 'Chr1'
assert len(seqs[0].sequence) == 1235
assert seqs[0].sequence.startswith('CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATC')
assert seqs[1].sequence.startswith('CTCGACCAGGACGATGAATGGGC')
def test_fastareader_lower():
with FastaReader(dpath("seq.fa"), case='lower') as fr:
seqs = list(fr)
assert seqs[0].name == 'Chr1'
assert len(seqs[0].sequence) == 1235
assert seqs[0].sequence.startswith('ccctaaaccctaaaccctaaaccctaaacctctgaatccttaatc')
assert seqs[1].sequence.startswith('ctcgaccaggacgatgaatgggc')
def test_fastareader_binary():
for wholefile in False, True:
print('wholefile:', wholefile)
with FastaReader(dpath("seq.fa"), binary=True, wholefile=wholefile, case='keep') as fr:
seqs1 = list(fr)
with FastaReader(dpath("seq.fa"), mode='rb', wholefile=wholefile, case='keep') as fr:
seqs2 = list(fr)
for seqs in seqs1, seqs2:
assert fr._file.closed
assert len(seqs) == 3
assert seqs[0].qualities is None
assert seqs[0].name == 'Chr1'
assert seqs[2].name == 'Chr3 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02'
assert len(seqs[0].sequence) == 1235
assert seqs[0].sequence.startswith(b'CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATC')
assert seqs[1].sequence.startswith(b'ctcgaccaggacgatgaatgggc')
assert seqs[2].sequence.endswith(b'AATCTTGCAAGTTCCAACTAATT')
def test_sequence_reader():
# should auto-detect FASTA vs FASTQ
with SequenceReader(dpath("seq.fa")) as sr:
assert sr.format == 'fasta'
with SequenceReader(dpath("seq.fastq")) as sr:
assert sr.format == 'fastq'
def test_fastareader_contextmanager():
with pytest.raises(ValueError):
fr = FastaReader(dpath("seq.fa"))
with fr as frw:
pass
with fr as frw:
pass
def test_fastq_header():
h = fastq_header(StringIO('@HWI-ST344:204:D14G8ACXX:8:1101:1638:2116 1:N:0:CGATGT'))
assert h.instrument == 'HWI-ST344'
assert h.run == 204
assert h.flowcell == 'D14G8ACXX'
assert h.lane == 8
assert h.barcode == 'CGATGT'
h = fastq_header(StringIO('@MISEQ:56:000000000-A4YM7:1:1101:15071:2257 1:N:0:CTTGTA'))
assert h.instrument == 'MISEQ'
assert h.run == 56
assert h.flowcell == '000000000-A4YM7'
assert h.lane == 1
assert h.barcode == 'CTTGTA'
h = fastq_header(StringIO('@HWI-ST552_0:4:1101:1179:1939#0/1'))
print(h)
assert h.instrument == 'HWI-ST552_0'
assert h.run is None
assert h.flowcell is None
assert h.lane == 4
assert h.barcode is None
h = fastq_header(StringIO('@HWI_ST139:8:1:1202:1874#GATCAG/1'))
assert h.instrument == 'HWI_ST139'
assert h.run is None
assert h.flowcell is None
assert h.lane == 8
assert h.barcode == 'GATCAG'
#h = fastq_header(StringIO('@FCD20MKACXX:8:1101:1215:2155#TCGTAAGC/1'))
#assert h.instrument is None
#assert h.run is None
#assert h.flowcell == 'FCD20MKACXX'
#assert h.lane == 8
#assert h.barcode == 'TCGTAAGC'
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