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import pysam
import unittest
import os
import gzip
import copy
import shutil
from TestUtils import check_url, BAM_DATADIR, get_temp_filename
class TestFastaFile(unittest.TestCase):
sequences = {
'chr1':
"CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGAACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTGTGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTCTTCTTA", # noqa
'chr2':
"TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATAAAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACCTCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGATGATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATAGCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAAAAAATATTTACAGTAACT", # noqa
}
def setUp(self):
self.file = pysam.FastaFile(os.path.join(BAM_DATADIR, "ex1.fa"))
def testFetch(self):
for id, seq in list(self.sequences.items()):
self.assertEqual(seq, self.file.fetch(id))
for x in range(0, len(seq), 10):
self.assertEqual(seq[x:x + 10], self.file.fetch(id, x, x + 10))
# test x:end
self.assertEqual(seq[x:], self.file.fetch(id, x))
# test 0:x
self.assertEqual(seq[:x], self.file.fetch(id, None, x))
# unknown sequence raises IndexError
self.assertRaises(KeyError, self.file.fetch, "chr12")
def testOutOfRangeAccess(self):
'''test out of range access.'''
# out of range access returns an empty string
for contig, s in self.sequences.items():
self.assertEqual(self.file.fetch(contig, len(s), len(s) + 1), "")
def testFetchErrors(self):
self.assertRaises(ValueError, self.file.fetch)
self.assertRaises(ValueError, self.file.fetch, "chr1", -1, 10)
self.assertRaises(ValueError, self.file.fetch, "chr1", 20, 10)
self.assertRaises(KeyError, self.file.fetch, "chr3", 0, 100)
def test_fetch_with_region_and_contig_raises_exception(self):
self.assertRaises(ValueError, self.file.fetch, "chr1", 10, 20, "chr1:11-20")
def test_fetch_with_region_is_equivalent(self):
self.assertEqual(self.file.fetch("chr1", 10, 20),
self.file.fetch(region="chr1:11-20"))
def testLength(self):
self.assertEqual(len(self.file), 2)
def testSequenceLengths(self):
self.assertEqual(1575, self.file.get_reference_length("chr1"))
self.assertEqual(1584, self.file.get_reference_length("chr2"))
def tearDown(self):
self.file.close()
class TestFastaFilePathIndex(unittest.TestCase):
filename = os.path.join(BAM_DATADIR, "ex1.fa")
data_suffix = ".fa"
def test_raise_exception_if_index_is_missing(self):
self.assertRaises(IOError,
pysam.FastaFile,
self.filename,
filepath_index="garbage" + self.data_suffix + ".fai")
def test_open_file_without_index_succeeds(self):
with pysam.FastaFile(self.filename) as inf:
self.assertEqual(len(inf), 2)
def test_open_file_with_explicit_index_succeeds(self):
with pysam.FastaFile(self.filename,
filepath_index=self.filename + ".fai") as inf:
self.assertEqual(len(inf), 2)
def test_open_file_with_explicit_abritrarily_named_index_succeeds(self):
tmpfilename = get_temp_filename(self.data_suffix)
shutil.copyfile(self.filename, tmpfilename)
filepath_index = self.filename + ".fai"
filepath_index_compressed = self.filename + ".gzi"
if not os.path.exists(filepath_index_compressed):
filepath_index_compressed = None
with pysam.FastaFile(tmpfilename,
filepath_index=filepath_index,
filepath_index_compressed=filepath_index_compressed) as inf:
self.assertEqual(len(inf), 2)
# index should not be auto-generated
self.assertFalse(os.path.exists(tmpfilename + ".fai"))
os.unlink(tmpfilename)
class TestFastaFilePathIndexCompressed(TestFastaFilePathIndex):
filename = os.path.join(BAM_DATADIR, "ex1.fa.gz")
data_suffix = ".fa.gz"
class TestFastxFileFastq(unittest.TestCase):
filetype = pysam.FastxFile
filename = "faidx_ex1.fq"
persist = True
def setUp(self):
self.file = self.filetype(os.path.join(BAM_DATADIR, self.filename),
persist=self.persist)
self.has_quality = self.filename.endswith('.fq')
def tearDown(self):
self.file.close()
def checkFirst(self, s):
# test first entry
self.assertEqual(s.sequence, "GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC")
self.assertEqual(s.name, "B7_589:1:101:825:28")
if self.has_quality:
self.assertEqual(s.quality, "<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;")
self.assertEqual(list(s.get_quality_array()),
[ord(x) - 33 for x in s.quality])
self.assertEqual(str(s),
"@B7_589:1:101:825:28\n"
"GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC\n"
"+\n"
"<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;")
else:
self.assertEqual(s.quality, None)
self.assertEqual(s.get_quality_array(), None)
self.assertEqual(str(s),
">B7_589:1:101:825:28\n"
"GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC")
def checkLast(self, s):
self.assertEqual(s.sequence, "TAATTGAAAAATTCATTTAAGAAATTACAAAATAT")
self.assertEqual(s.name, "EAS56_65:8:64:507:478")
if self.has_quality:
self.assertEqual(s.quality, "<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<")
self.assertEqual(list(s.get_quality_array()),
[ord(x) - 33 for x in s.quality])
else:
self.assertEqual(s.quality, None)
self.assertEqual(s.get_quality_array(), None)
def testCounts(self):
self.assertEqual(len([x for x in self.file]), 3270)
def testMissingFile(self):
self.assertRaises(IOError, self.filetype, "nothere.fq")
def testSequence(self):
first = self.file.__next__()
self.checkFirst(first)
for last in self.file:
pass
self.checkLast(last)
# test for persistence
if self.persist:
self.checkFirst(first)
else:
self.checkLast(first)
def testManager(self):
with self.filetype(os.path.join(BAM_DATADIR, self.filename),
persist=self.persist) as inf:
first = inf.__next__()
self.checkFirst(first)
for last in inf:
pass
self.checkLast(last)
self.assertEqual(inf.closed, True)
# Test for backwards compatibility
class TestFastqFileFastq(TestFastxFileFastq):
filetype = pysam.FastqFile
# Test for backwards compatibility
class TestFastxFileFasta(TestFastxFileFastq):
filetype = pysam.FastqFile
filename = "faidx_ex1.fa"
class TestFastxFileFastqStream(TestFastxFileFastq):
persist = False
class TestFastxFileWithEmptySequence(unittest.TestCase):
"""see issue 204:
iteration over fastq file with empty sequence stops prematurely
"""
filetype = pysam.FastxFile
filename = "faidx_empty_seq.fq.gz"
def testIteration(self):
fn = os.path.join(BAM_DATADIR, self.filename)
with gzip.open(fn) as inf:
ref_num = len(list(inf)) / 4
with self.filetype(fn) as f:
l = len(list(f))
self.assertEqual(ref_num, l)
class TestRemoteFileFTP(unittest.TestCase):
'''test remote access.
'''
url = ("ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/"
"GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa")
def testFTPView(self):
if not check_url(self.url):
return
try:
with pysam.Fastafile(self.url) as f:
self.assertEqual(
len(f.fetch("chr1", 0, 1000)),
1000)
except (OSError, IOError):
pass
def test_sequence_lengths_are_available(self):
if not check_url(self.url):
return
try:
with pysam.Fastafile(self.url) as f:
self.assertEqual(len(f.references), 3366)
self.assertTrue("chr1" in f.references)
self.assertEqual(f.lengths[0],
248956422)
self.assertEqual(f.get_reference_length("chr1"),
248956422)
except (OSError, IOError):
pass
class TestFastqRecord(unittest.TestCase):
filetype = pysam.FastxFile
filename = "faidx_ex1.fq"
def setUp(self):
with self.filetype(os.path.join(BAM_DATADIR, self.filename), persist=True) as inf:
self.record = next(inf)
def test_fastx_record_sequence_can_be_modified(self):
old_sequence = self.record.sequence
new_record = copy.copy(self.record)
new_sequence = "AAAC"
new_record.set_sequence(new_sequence)
self.assertEqual(str(new_record), ">{}\n{}".format(
self.record.name, new_sequence))
self.assertEqual(self.record.sequence, old_sequence)
self.assertEqual(new_record.sequence, new_sequence)
def test_fastx_record_name_can_be_modified(self):
old_name = self.record.name
new_name = "new_name"
new_record = copy.copy(self.record)
new_record.set_name(new_name)
self.assertEqual(new_record.name, new_name)
self.assertEqual(self.record.name, old_name)
def test_fastx_record_fail_if_name_is_None(self):
self.assertRaises(ValueError,
self.record.set_name,
None)
def test_fastx_record_comment_can_be_modified(self):
old_comment = self.record.comment
new_comment = "this is a new comment"
new_record = copy.copy(self.record)
new_record.set_comment(new_comment)
self.assertEqual(new_record.comment, new_comment)
self.assertEqual(self.record.comment, old_comment)
def test_fastx_record_comment_can_be_None(self):
old_comment = self.record.comment
new_comment = None
new_record = copy.copy(self.record)
new_record.set_comment(new_comment)
self.assertEqual(new_record.comment, new_comment)
self.assertEqual(self.record.comment, old_comment)
def test_fastx_record_quality_can_be_modified(self):
old_quality = self.record.quality
new_quality = "A" * len(old_quality)
new_record = copy.copy(self.record)
new_record.set_sequence(self.record.sequence, new_quality)
self.assertEqual(new_record.quality, new_quality)
self.assertEqual(self.record.quality, old_quality)
def test_fastx_record_fail_if_quality_is_wrong_length(self):
self.assertRaises(ValueError,
self.record.set_sequence,
self.record.sequence, self.record.quality * 2)
def test_fastx_record_can_be_created_from_scratch(self):
fastx_record = pysam.FastxRecord()
self.assertRaises(ValueError,
str,
fastx_record)
fastx_record.set_name("name")
self.assertRaises(ValueError,
str,
fastx_record)
fastx_record.set_sequence("sequence")
self.assertEqual(str(fastx_record), ">name\nsequence")
if __name__ == "__main__":
unittest.main()
|
