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import pytest
import sys
import os
import glob
import sysconfig
from pathlib import Path
build_dir = "build/lib.%s-%s" % (sysconfig.get_platform(), sys.version[0:3])
sys.path.insert(0, os.path.join(os.getcwd(), build_dir))
import HTSeq
def test_fasta_parser(data_folder):
print("Test Fasta parser")
for seq in HTSeq.FastaReader(data_folder+'fastaExLong.fa'):
pass
print("Test passed")
print("Test Fasta parser (raw iterator)")
for seq in HTSeq.FastaReader(data_folder+'fastaExLong.fa',
raw_iterator=True):
pass
print("Test passed")
print('Test Fasta parser (with statement)')
with HTSeq.FastaReader(data_folder+'fastaExLong.fa') as f:
for seq in f:
pass
print('Test passed')
print('Test Fasta parser (with statement and file handle)')
with open(data_folder+'fastaExLong.fa') as fraw:
f = HTSeq.FastaReader(fraw)
for seq in f:
pass
print('Test passed')
def test_fastq_parser(data_folder):
print("Test Fastq parser")
for seq in HTSeq.FastqReader(data_folder+'fastqEx.fastq'):
pass
print("Test passed")
print("Test Fastq parser on gzip input")
for seq in HTSeq.FastqReader(data_folder+'fastqExgzip.fastq.gz'):
pass
print("Test passed")
print("Test Fastq parser on gzip input (raw iterator)")
for seq in HTSeq.FastqReader(data_folder+'fastqExgzip.fastq.gz',
raw_iterator=True):
pass
print("Test passed")
print('Test Fastq parser (with statement)')
with HTSeq.FastqReader(data_folder+'fastqExgzip.fastq.gz') as f:
for seq in f:
pass
print('Test passed')
print('Test Fastq parser (with statement and file handle)')
import gzip
with gzip.open(data_folder+'fastqExgzip.fastq.gz', 'rt') as fraw:
f = HTSeq.FastqReader(fraw)
for seq in f:
pass
print('Test passed')
def test_path_like_reading(data_folder):
data_file = Path(data_folder) / 'yeast_RNASeq_excerpt.sam'
print('Test BAM reader with pathlib.Path')
bamfile = HTSeq.BAM_Reader(data_file)
for read in bamfile:
pass
print('Test passed')
print('Test BAM reader (with statement) with pathlib.Path')
with HTSeq.BAM_Reader(data_file) as f:
for read in f:
pass
print('Test passed')
def test_open_handle_reading(data_folder):
data_file = Path(data_folder) / 'yeast_RNASeq_excerpt.sam'
print('Test BAM reader with open handle')
with open(data_file) as f:
reader = HTSeq.BAM_Reader(f)
for read in reader:
pass
print('Test passed')
def test_unreadable_object_reading():
unreadable_object = object()
print('Test BAM reader with unreadable object')
with pytest.raises(TypeError):
reader = HTSeq.BAM_Reader(unreadable_object)
for read in reader:
pass
print('Test passed')
print('Test BAM reader with unreadable object, context manager')
with pytest.raises(TypeError):
with HTSeq.BAM_Reader(unreadable_object) as reader:
for read in reader:
pass
print('Test passed')
def test_bam_reader(data_folder):
print('Test BAM reader')
bamfile = HTSeq.BAM_Reader(data_folder+"yeast_RNASeq_excerpt.sam")
for read in bamfile:
pass
print('Test passed')
print('Test BAM reader (with statement)')
with HTSeq.BAM_Reader(data_folder+"yeast_RNASeq_excerpt.sam") as f:
for read in f:
pass
print('Test passed')
def test_bam_inconsistent_mate(data_folder):
print('Test inconsistent BAM file')
bamfile = HTSeq.BAM_Reader(data_folder+"inconsistent_mate.bam")
for read in bamfile:
pass
print("Test passed")
def test_bam_optional_field(data_folder):
print('Test optional fields in BAM alignment')
bamfile = HTSeq.BAM_Reader(data_folder+"inconsistent_mate.bam")
for read in bamfile:
read.has_optional_field('NO')
break
print("Test passed")
def test_GFF3(data_folder):
print('Test GFF3 reader')
with HTSeq.GFF_Reader(data_folder+'GCF_000001405.39_GRCh38.p13_genomic_subsample.gff.gz') as reader:
for line in reader:
pass
print("Test passed")
def test_pickle():
import pickle
print('Test pickling and inpickling')
pickles = [
{'name': 'HTSeq.Sequence',
'object': HTSeq.Sequence(b'ACTG', 'sequence'),
'assert_properties': ('seq', 'name', 'descr')},
]
for pic in pickles:
print('Pickling '+pic['name'])
pickled = pickle.dumps(pic['object'])
print('Done')
print('Unpickling '+pic['name'])
unpick = pickle.loads(pickled)
print('Done')
if 'assert_properties' in pic:
print('Checking serialized/deserialized')
for prop in pic['assert_properties']:
assert getattr(pic['object'], prop) == getattr(unpick, prop)
print('Done')
print("Test passed")
def test_bamfile_nosq(data_folder):
print('Test parsing BAM file with no SQ field (e.g. PacBio)')
bamfile = HTSeq.BAM_Reader(
data_folder+"short_test_ccs.bam",
check_sq=False)
for read in bamfile:
pass
print("Test passed")
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