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Modify IO to provide options of linking to genome sequence path
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@YinHoon
YinHoon committed Dec 12, 2018
1 parent 63470b0 commit 3e797d6
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Showing 3 changed files with 127 additions and 58 deletions.
25 changes: 25 additions & 0 deletions tests/fixtures/eukaryote_seq.fna.fai
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chromosome1 840 13 70 71
chromosome2 630 878 70 71
chromosome3 560 1530 70 71
chromosome4 630 2111 70 71
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chromosome6 910 3486 70 71
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chromosome11 700 7387 70 71
chromosome12 630 8111 70 71
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chromosome15 1330 10354 70 71
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chromosome18 1120 13449 70 71
chromosome19 700 14599 70 71
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chromosome22 1120 17623 70 71
chromosomeX 1120 18772 70 71
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chromosomeMT 700 20929 70 71
97 changes: 69 additions & 28 deletions tests/test_io.py
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Expand Up @@ -10,6 +10,8 @@
from wc_kb import core, prokaryote_schema
from wc_kb import io
import Bio.Seq
import Bio.SeqRecord
import filecmp
import obj_model.io
import os
import random
Expand All @@ -22,21 +24,26 @@
class TestIO(unittest.TestCase):

def setUp(self):
self.dir = tempfile.mkdtemp()
self.seq_path = os.path.join(self.dir, 'seq.fna')

self.kb = kb = core.KnowledgeBase(id='genus_species', name='Genus species', version='0.0.1')

cell = kb.cell = core.Cell(id='genus_species_cell')

dna_seqs = []
for i_chr in range(5):
dna = core.DnaSpeciesType(id='chr_{}'.format(i_chr + 1))
dna = core.DnaSpeciesType(id='chr_{}'.format(i_chr + 1), sequence_path=self.seq_path)
cell.species_types.append(dna)

seq_len = random.randint(100, 200)
bases = 'ACGT'
seq = ''
for i_nt in range(seq_len):
seq += bases[random.randint(0, 3)]
dna.seq = Bio.Seq.Seq(seq)

dna_seqs.append(Bio.SeqRecord.SeqRecord(
Bio.Seq.Seq(seq), dna.id))

for i_trn in range(5):
trn = prokaryote_schema.TranscriptionUnitLocus(id='tu_{}_{}'.format(i_chr + 1, i_trn + 1))
trn.cell = cell
Expand All @@ -45,32 +52,35 @@ def setUp(self):
trn.end = ((trn.start + random.randint(1, 200) - 1) % seq_len) + 1
trn.strand = core.PolymerStrand.positive

self.dir = tempfile.mkdtemp()
with open(self.seq_path, 'w') as file:
writer = Bio.SeqIO.FastaIO.FastaWriter(
file, wrap=70, record2title=lambda record: record.id)
writer.write_file(dna_seqs)

def tearDown(self):
shutil.rmtree(self.dir)

def test_write_read(self):
core_path = os.path.join(self.dir, 'core.xlsx')
seq_path = os.path.join(self.dir, 'seq.fna')
core_path = os.path.join(self.dir, 'core.xlsx')

writer = io.Writer()
writer.run(self.kb, core_path, seq_path, set_repo_metadata_from_path=False)
writer.run(self.kb, core_path, set_repo_metadata_from_path=False)

reader = io.Reader()
kb = reader.run(core_path, seq_path)
kb = reader.run(core_path, self.seq_path)

core_path = os.path.join(self.dir, 'core2.xlsx')
seq_path = os.path.join(self.dir, 'seq2.fna')
writer.run(kb, core_path, seq_path, set_repo_metadata_from_path=False)

self.assertTrue(self.kb.is_equal(kb))
self.assertTrue(filecmp.cmp(self.seq_path, seq_path, shallow=False))

def test_read_write_prokaryote(self):
fixtures = os.path.join(os.path.dirname(__file__), 'fixtures')
core_path = os.path.join(fixtures, 'core.xlsx')
seq_path = os.path.join(fixtures, 'seq.fna')

reader = io.Reader()
kb = reader.run(core_path, seq_path)

Expand All @@ -80,15 +90,16 @@ def test_read_write_prokaryote(self):
writer = io.Writer()
writer.run(kb, tmp_core_path, tmp_seq_path, set_repo_metadata_from_path=False)

tmp_kb = reader.run(tmp_core_path, tmp_seq_path)
tmp_kb = reader.run(tmp_core_path, seq_path)

self.assertTrue(kb.is_equal(tmp_kb))
self.assertTrue(filecmp.cmp(tmp_seq_path, seq_path, shallow=False))

def test_read_write_eukaryote(self):
fixtures = os.path.join(os.path.dirname(__file__), 'fixtures')
core_path = os.path.join(fixtures, 'eukaryote_core.xlsx')
seq_path = os.path.join(fixtures, 'eukaryote_seq.fna')

reader = io.Reader()
kb = reader.run(core_path, seq_path, schema=False)

Expand All @@ -98,9 +109,30 @@ def test_read_write_eukaryote(self):
writer = io.Writer()
writer.run(kb, tmp_core_path, tmp_seq_path, schema=False, set_repo_metadata_from_path=False)

tmp_kb = reader.run(tmp_core_path, tmp_seq_path, schema=False)
tmp_kb = reader.run(tmp_core_path, seq_path, schema=False)

self.assertTrue(kb.is_equal(tmp_kb))
self.assertTrue(filecmp.cmp(tmp_seq_path, seq_path, shallow=False))

def test_rewrite_seq_path_in_read_write(self):
path_core_1 = os.path.join(self.dir, 'core_1.xlsx')
path_core_2 = os.path.join(self.dir, 'core_2.xlsx')
path_seq_1 = os.path.join(self.dir, 'seq_1.fna')
path_seq_2 = os.path.join(self.dir, 'seq_2.fna')

io.Writer().run(self.kb, path_core_1, path_seq_1, set_repo_metadata_from_path=False)
kb1 = io.Reader().run(path_core_1, path_seq_1)
kb2 = io.Reader().run(path_core_1, path_seq_1, rewrite_seq_path=False)
self.assertFalse(kb1.is_equal(self.kb))
self.assertTrue(kb2.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_1, self.seq_path, shallow=False))

io.Writer().run(self.kb, path_core_2, path_seq_2, rewrite_seq_path=True, set_repo_metadata_from_path=False)
kb3 = io.Reader().run(path_core_2, self.seq_path)
kb4 = io.Reader().run(path_core_2, self.seq_path, rewrite_seq_path=False)
self.assertFalse(kb3.is_equal(self.kb))
self.assertTrue(kb4.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_2, self.seq_path, shallow=False))

def test_write_with_repo_md(self):
_, core_path = tempfile.mkstemp(suffix='.xlsx', dir='.')
Expand All @@ -122,10 +154,12 @@ def test_write_with_repo_md(self):

def test_write_without_cell_relationships(self):
core_path = os.path.join(self.dir, 'core.xlsx')
seq_path = os.path.join(self.dir, 'seq.fna')
seq_path = os.path.join(self.dir, 'test_seq.fna')

dna = core.DnaSpeciesType(id='chr_x')
dna.seq = Bio.Seq.Seq('ACGT')
with open(seq_path, 'w') as file:
file.write('>chr_x\nACGT\n')

dna = core.DnaSpeciesType(id='chr_x', sequence_path=seq_path)
self.kb.cell.species_types.append(dna)

trn = prokaryote_schema.TranscriptionUnitLocus(id='tu_x_0')
Expand All @@ -138,8 +172,8 @@ def test_write_without_cell_relationships(self):

def test_write_read_sloppy(self):
core_path = os.path.join(self.dir, 'core.xlsx')
seq_path = os.path.join(self.dir, 'seq.fna')

seq_path = os.path.join(self.dir, 'test_seq.fna')
writer = io.Writer()
writer.run(self.kb, core_path, seq_path, set_repo_metadata_from_path=False)

Expand All @@ -150,16 +184,17 @@ def test_write_read_sloppy(self):

reader = io.Reader()
with self.assertRaisesRegex(ValueError, "The columns of worksheet 'Knowledge base' must be defined in this order"):
kb = reader.run(core_path, seq_path)
kb = reader.run(core_path, seq_path, strict=False)
kb = reader.run(core_path, self.seq_path)
kb = reader.run(core_path, self.seq_path, strict=False)

self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(self.seq_path, seq_path, shallow=False))

def test_reader_no_kb(self):
core_path = os.path.join(self.dir, 'core.xlsx')
obj_model.io.WorkbookWriter().run(core_path, [], io.PROKARYOTE_MODEL_ORDER, include_all_attributes=False)

seq_path = os.path.join(self.dir, 'seq.fna')
seq_path = os.path.join(self.dir, 'test_seq.fna')
with open(seq_path, 'w') as file:
pass

Expand All @@ -177,7 +212,7 @@ def test_reader_error_multiple_kbs(self):
core_path = os.path.join(self.dir, 'core.xlsx')
obj_model.io.WorkbookWriter().run(core_path, [kb1, kb2], io.PROKARYOTE_MODEL_ORDER, include_all_attributes=False)

seq_path = os.path.join(self.dir, 'seq.fna')
seq_path = os.path.join(self.dir, 'test_seq.fna')
with open(seq_path, 'w') as file:
pass

Expand All @@ -191,7 +226,7 @@ def test_reader_error_no_cell(self):
core_path = os.path.join(self.dir, 'core.xlsx')
obj_model.io.WorkbookWriter().run(core_path, [kb, dna], io.PROKARYOTE_MODEL_ORDER, include_all_attributes=False)

seq_path = os.path.join(self.dir, 'seq.fna')
seq_path = os.path.join(self.dir, 'test_seq.fna')
with open(seq_path, 'w') as file:
pass

Expand All @@ -206,7 +241,7 @@ def test_reader_error_multiple_cells(self):
core_path = os.path.join(self.dir, 'core.xlsx')
obj_model.io.WorkbookWriter().run(core_path, [kb, cell1, cell2], io.PROKARYOTE_MODEL_ORDER, include_all_attributes=False)

seq_path = os.path.join(self.dir, 'seq.fna')
seq_path = os.path.join(self.dir, 'test_seq.fna')
with open(seq_path, 'w') as file:
pass

Expand All @@ -222,14 +257,17 @@ def test_convert(self):
path_seq_3 = os.path.join(self.dir, 'seq_3.fna')

io.Writer().run(self.kb, path_core_1, path_seq_1, set_repo_metadata_from_path=False)
self.assertTrue(filecmp.cmp(path_seq_1, self.seq_path, shallow=False))

io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2)
kb = io.Reader().run(path_core_2, path_seq_2)
kb = io.Reader().run(path_core_2, self.seq_path)
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_1, path_seq_2, shallow=False))

io.convert(path_core_2, path_seq_2, path_core_3, path_seq_3)
kb = io.Reader().run(path_core_3, path_seq_3)
kb = io.Reader().run(path_core_3, self.seq_path)
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_2, path_seq_3, shallow=False))

def test_convert_sloppy(self):
path_core_1 = os.path.join(self.dir, 'core_1.xlsx')
Expand All @@ -240,6 +278,7 @@ def test_convert_sloppy(self):
path_seq_3 = os.path.join(self.dir, 'seq_3.fna')

io.Writer().run(self.kb, path_core_1, path_seq_1, set_repo_metadata_from_path=False)
self.assertTrue(filecmp.cmp(path_seq_1, self.seq_path, shallow=False))

wb = wc_utils.workbook.io.read(path_core_1)
row = wb['Knowledge base'].pop(0)
Expand All @@ -249,12 +288,14 @@ def test_convert_sloppy(self):
with self.assertRaisesRegex(ValueError, "The columns of worksheet 'Knowledge base' must be defined in this order"):
io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2)
io.convert(path_core_1, path_seq_1, path_core_2, path_seq_2, strict=False)
kb = io.Reader().run(path_core_2, path_seq_2)
kb = io.Reader().run(path_core_2, self.seq_path)
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_1, path_seq_2, shallow=False))

io.convert(path_core_2, path_seq_2, path_core_3, path_seq_3)
kb = io.Reader().run(path_core_3, path_seq_3)
kb = io.Reader().run(path_core_3, self.seq_path)
self.assertTrue(kb.is_equal(self.kb))
self.assertTrue(filecmp.cmp(path_seq_2, path_seq_3, shallow=False))

def test_create_template(self):
path_core = os.path.join(self.dir, 'template.xlsx')
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