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import tempfile
import os
import pytest
from io import StringIO
from pbcore.io import GffWriter, Gff3Record, GffReader
from pbcore.io.GffIO import merge_gffs, merge_gffs_sorted, sort_gff
from pbcore import data
def rm_out(fname):
if os.path.exists(fname):
os.remove(fname)
class TestGff3Record:
RECORD = Gff3Record("chr1", 10, 11, "insertion",
attributes=[("cat", "1"), ("dog", "2")])
def test_str(self):
assert "chr1\t.\tinsertion\t10\t11\t.\t.\t.\tcat=1;dog=2" == str(
self.RECORD)
def test_modification(self):
record = self.RECORD.copy()
record.dog = 3
record.cat = 4
record.mouse = 5
record.start = 100
record.end = 110
assert "chr1\t.\tinsertion\t100\t110\t.\t.\t.\tcat=4;dog=3;mouse=5" == str(
record)
def test_fromString(self):
newRecord = Gff3Record.fromString(str(self.RECORD))
assert str(self.RECORD) == str(newRecord)
def test_get(self):
"""
Verify field access behavior
"""
record = self.RECORD
record.dog = 3
record.cat = 4
record.mouse = 5
record.start = 100
record.end = 110
assert 3 == record.dog
assert 100 == record.start
with pytest.raises(AttributeError):
record.god
assert 3 == record.get("dog")
assert record.get("god") is None
assert 100 == record.get("start", 100)
class TestGffReader:
RAWFILE = open(data.getGff3())
READER = GffReader(data.getGff3())
def test_headers(self):
assert ["##gff-version 3",
"##pacbio-variant-version 2.1",
"##date Sat Mar 22 12:16:13 2014",
"##feature-ontology http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12",
"##source GenomicConsensus 0.8.0",
"##source-commandline /Users/dalexander/.virtualenvs/VE/bin/variantCaller.py --algorithm=plurality -q20 -x5 pbcore/data/aligned_reads_1.cmp.h5 -r /Users/dalexander/Data/lambdaNEB.fa -o /tmp/v.gff",
"##source-alignment-file /Users/dalexander/Dropbox/Sources/git/pbcore/pbcore/data/aligned_reads_1.cmp.h5",
"##source-reference-file /Users/dalexander/Data/lambdaNEB.fa",
"##sequence-region lambda_NEB3011 1 48502"] == self.READER.headers
def test__iter__(self):
records = list(self.READER)
rawLines = self.RAWFILE.readlines()[9:]
for record, rawLine in zip(records, rawLines):
# No newlines or whitespace allowed in records
assert str(record).strip() == str(record)
# Make sure record matches line
assert rawLine.strip() == str(record)
class TestGffWriter:
RECORD1 = Gff3Record("chr1", 10, 11, "insertion",
attributes=[("cat", "1"), ("dog", "2")])
RECORD2 = Gff3Record("chr1", 200, 201, "substitution",
attributes=[("mouse", "1"), ("moose", "2")])
def setup_method(self):
self.outfile = StringIO()
self.gffWriter = GffWriter(self.outfile)
def test_writeHeader(self):
self.gffWriter.writeHeader("##foo bar")
assert "##gff-version 3\n##foo bar\n" == self.outfile.getvalue()
def test_writeRecord(self):
self.gffWriter.writeRecord(self.RECORD1)
self.gffWriter.writeRecord(self.RECORD2)
expected = ("##gff-version 3\n" +
"chr1\t.\tinsertion\t10\t11\t.\t.\t.\tcat=1;dog=2\n" +
"chr1\t.\tsubstitution\t200\t201\t.\t.\t.\tmouse=1;moose=2\n")
assert expected == self.outfile.getvalue()
class TestGffSorting:
GFF_DATA = ["""\
##gff-version 3
##source ipdSummary
##source-commandline ipdSummary etc.
##sequence-region lambda_NEB3011 1 48502
chr1\tkinModCall\tmodified_base\t32580\t32580\t32\t-\t.\tcoverage=94;context=AATGGCATCGTTCCGGTGGTGGGCGTTGATGGCTGGTCCCG;IPDRatio=1.75
chr1\tkinModCall\tmodified_base\t32766\t32766\t42\t-\t.\tcoverage=170;context=GCTGGGAAGCTGGCTGAACGTGTCGGCATGGATTCTGTCGA;IPDRatio=1.70
chr1\tkinModCall\tmodified_base\t32773\t32773\t54\t-\t.\tcoverage=154;context=AACGCTGGCTGGGAAGCTGGCTGAACGTGTCGGCATGGATT;IPDRatio=2.65""", """\
##gff-version 3
##source ipdSummary
##source-commandline ipdSummary etc.
##sequence-region lambda_NEB3011 1 48502
chr2\tkinModCall\tmodified_base\t1200\t1200\t47\t-\t.\tcoverage=109;context=ACTTTTCACGGTAGTTTTTTGCCGCTTTACCGCCCAGGCAC;IPDRatio=1.89
chr2\tkinModCall\tmodified_base\t1786\t1786\t36\t-\t.\tcoverage=153;context=TCCCACGTCTCACCGAGCGTGGTGTTTACGAAGGTTTTACG;IPDRatio=1.67
chr2\tkinModCall\tmodified_base\t1953\t1953\t39\t+\t.\tcoverage=148;context=AATGCGCGTATGGGGATGGGGGCCGGGTGAGGAAAGCTGGC;IPDRatio=1.86""", """\
chr1\tkinModCall\tmodified_base\t16204\t16204\t31\t-\t.\tcoverage=119;context=CCCGCGCAGATGATAATTACGGCTCACCTGCTGGCTGCCGA;IPDRatio=1.80
chr1\tkinModCall\tmodified_base\t16302\t16302\t33\t+\t.\tcoverage=108;context=TGGGACGGAACGTTTAAACCGGCATACAGCAACAACATGGC;IPDRatio=1.81
chr1\tkinModCall\tmodified_base\t16348\t16348\t42\t-\t.\tcoverage=115;context=CCCCATGCCGTAGCGCGGATGGGTCAGCATATCCCACAGAC;IPDRatio=1.82""", ]
SORTED_START = [
('chr1', 16204), ('chr1', 16302), ('chr1', 16348),
('chr1', 32580), ('chr1', 32766), ('chr1', 32773),
('chr2', 1200), ('chr2', 1786), ('chr2', 1953),
]
@classmethod
def setup_class(cls):
cls.files = []
cls.combined = "tmp_pbcore_all.gff"
with open(cls.combined, "w") as f_all:
for i in range(3):
file_name = "tmp_pbcore_%d.gff" % i
with open(file_name, "w") as f:
f.write(cls.GFF_DATA[i])
cls.files.append(file_name)
for line in cls.GFF_DATA[i].splitlines():
if line.startswith("#"):
if i == 0:
f_all.write(line+"\n")
else:
f_all.write(line+"\n")
@classmethod
def teardown_class(cls):
for file_name in cls.files:
if os.path.exists(file_name):
os.remove(file_name)
if os.path.exists(cls.combined):
os.remove(cls.combined)
def test_merge_gffs(self):
gff_out = "tmp_pbcore_merge.gff"
merge_gffs(self.files, gff_out)
n_rec = 0
for fn in self.files:
with GffReader(fn) as f:
n_rec += len([rec for rec in f])
with GffReader(gff_out) as f:
assert f.headers == [
"##gff-version 3",
"##source ipdSummary",
"##sequence-region lambda_NEB3011 1 48502",
]
n_rec_merged = len([rec for rec in f])
assert n_rec == n_rec_merged
rm_out(gff_out)
def test_merge_gffs_sorted(self):
gff_out = "tmp_pbcore_merged_sorted.gff"
merge_gffs_sorted(self.files, gff_out)
with GffReader(gff_out) as f:
start = [(rec.seqid, rec.start) for rec in f]
assert start == self.SORTED_START
rm_out(gff_out)
def test_sort_gff(self):
gff_out = sort_gff(self.combined)
with GffReader(gff_out) as f:
start = [(rec.seqid, rec.start) for rec in f]
assert start == self.SORTED_START
rm_out(gff_out)
def test_empty_file(self):
gff_tmp = tempfile.NamedTemporaryFile(suffix=".gff").name
with open(gff_tmp, "w") as f:
f.write("##gff-version 3\n")
f.write("##source ipdSummary\n")
f.write("##sequence-region lambda_NEB3011 1 48502")
gff_out = tempfile.NamedTemporaryFile(suffix=".gff").name
merge_gffs(self.files + [gff_tmp], gff_out)
rm_out(gff_out)
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