def test_records_begin(self):
recs = {}
recs[0] = SeqRecord(Seq("TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAA"
"CACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTA"
"AAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCAT"
"AGAAGATGACATAATGTATTTTCCTTTTGGTT"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={"start": 3009319,
"srcSize": 129993255,
"strand": 1,
"size": 162})
recs[1] = SeqRecord(Seq("TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGG"
"TTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCA"
"GAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCAT"
"GGAAACTGATGTCAAATACTTTCCCTTTGGTT"),
id="oryCun1.scaffold_133159",
name="oryCun1.scaffold_133159",
description="",
annotations={"start": 11087,
"srcSize": 13221,
"strand": 1,
"size": 164})
fetched_recs = self.idx._get_record(34)
for i in range(2):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
def loop(self, filename, format):
original_records = list(SeqIO.parse(open(filename, "rU"), format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver = DBDRIVER,
user = DBUSER, passwd = DBPASSWD,
host = DBHOST, db = TESTDB)
db_name = "test_loop_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
#Now read them back...
biosql_records = [db.lookup(name=rec.name)
for rec in original_records]
#And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
#Now write to a handle...
handle = StringIO()
SeqIO.write(biosql_records, handle, "gb")
#Now read them back...
handle.seek(0)
new_records = list(SeqIO.parse(handle, "gb"))
#And check they still agree
self.assertEqual(len(new_records), len(original_records))
for old, new in zip(original_records, new_records):
#TODO - remove this hack because we don't yet write these (yet):
for key in ["comment", "references", "db_source"]:
if key in old.annotations and key not in new.annotations:
del old.annotations[key]
self.assertTrue(compare_record(old, new))
#Done
server.close()
def get_raw_check(self, filename, format, alphabet):
if format in SeqIO._BinaryFormats:
#This means SFF at the moment, which does not get
#implement the get_raw method
return
handle = open(filename, "rU")
raw_file = handle.read()
handle.close()
#Also checking the key_function here
id_list = [rec.id.lower() for rec in \
SeqIO.parse(filename, format, alphabet)]
rec_dict = SeqIO.index(filename, format, alphabet,
key_function = lambda x : x.lower())
self.assertEqual(set(id_list), set(rec_dict.keys()))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assert_(key in rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assert_(raw.strip())
self.assert_(raw in raw_file)
if format in ["ig"]:
#These have a header structure and can't be parsed
#individually (at least, not right now).
continue
rec1 = rec_dict[key]
rec2 = SeqIO.read(StringIO(raw), format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
def get_raw_check(self, filename, format, alphabet):
handle = open(filename, "rb")
raw_file = handle.read()
handle.close()
#Also checking the key_function here
id_list = [rec.id.lower() for rec in \
SeqIO.parse(filename, format, alphabet)]
rec_dict = SeqIO.index(filename, format, alphabet,
key_function = lambda x : x.lower())
self.assertEqual(set(id_list), set(rec_dict.keys()))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assertTrue(key in rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assertTrue(raw.strip())
self.assertTrue(raw in raw_file)
rec1 = rec_dict[key]
#Following isn't very elegant, but it lets me test the
#__getitem__ SFF code is working.
if format in SeqIO._BinaryFormats:
handle = BytesIO(raw)
else:
handle = StringIO(_bytes_to_string(raw))
if format == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False)
elif format == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True)
elif format == "uniprot-xml":
self.assertTrue(raw.startswith(_as_bytes("<entry ")))
self.assertTrue(raw.endswith(_as_bytes("</entry>")))
#Currently the __getitem__ method uses this
#trick too, but we hope to fix that later
raw = """<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % _bytes_to_string(raw)
handle = StringIO(raw)
rec2 = SeqIO.read(handle, format, alphabet)
else:
rec2 = SeqIO.read(handle, format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict._proxy._handle.close() #TODO - Better solution
del rec_dict
def test_multi_ex_index(self):
"""Index SwissProt text and uniprot XML versions of several examples."""
txt_list = list(SeqIO.parse("SwissProt/multi_ex.txt", "swiss"))
xml_list = list(SeqIO.parse("SwissProt/multi_ex.xml", "uniprot-xml"))
ids = [x.strip() for x in open("SwissProt/multi_ex.list")]
txt_index = SeqIO.index("SwissProt/multi_ex.txt", "swiss")
xml_index = SeqIO.index("SwissProt/multi_ex.xml", "uniprot-xml")
self.assertEqual(sorted(txt_index), sorted(ids))
self.assertEqual(sorted(xml_index), sorted(ids))
#Check SeqIO.parse() versus SeqIO.index() for plain text "swiss"
for old in txt_list:
new = txt_index[old.id]
compare_record(old, new)
#Check SeqIO.parse() versus SeqIO.index() for XML "uniprot-xml"
for old in xml_list:
new = xml_index[old.id]
compare_record(old, new)
def check(self, t_format, t_filename, t_count=1):
db = self.db
iterator = SeqIO.parse(handle=open(t_filename, "r"), format=t_format)
count = db.load(iterator)
assert count == t_count
self.server.commit()
iterator = SeqIO.parse(handle=open(t_filename, "r"), format=t_format)
for record in iterator:
#print " - %s, %s" % (checksum_summary(record), record.id)
key = record.name
#print " - Retrieving by name/display_id '%s'," % key,
db_rec = db.lookup(name=key)
compare_record(record, db_rec)
db_rec = db.lookup(display_id=key)
compare_record(record, db_rec)
key = record.id
if key.count(".") == 1 and key.split(".")[1].isdigit():
#print " - Retrieving by version '%s'," % key,
db_rec = db.lookup(version=key)
compare_record(record, db_rec)
if "accessions" in record.annotations:
#Only expect FIRST accession to work!
key = record.annotations["accessions"][0]
assert key, "Blank accession in annotation %s" % repr(record.annotations)
if key != record.id:
#print " - Retrieving by accession '%s'," % key,
db_rec = db.lookup(accession=key)
compare_record(record, db_rec)
if "gi" in record.annotations:
key = record.annotations['gi']
if key != record.id:
#print " - Retrieving by GI '%s'," % key,
db_rec = db.lookup(primary_id=key)
compare_record(record, db_rec)
def check_rewrite(self, filename):
old = SeqIO.read(filename, "embl")
#TODO - Check these properties:
old.dbxrefs = []
old.annotations['accessions'] = old.annotations['accessions'][:1]
del old.annotations['references']
buffer = StringIO()
self.assertEqual(1, SeqIO.write(old, buffer, "embl"))
buffer.seek(0)
new = SeqIO.read(buffer, "embl")
self.assertTrue(compare_record(old, new))
iterator = SeqIO.parse(handle=open(t_filename,"r"), format=t_format)
count = db.load(iterator)
assert count == t_count
#print " - Committing %i records" % count
server.commit()
iterator = SeqIO.parse(handle=open(t_filename,"r"), format=t_format)
for record in iterator :
print " - %s, %s" % (checksum_summary(record), record.id)
key = record.name
print " - Retrieving by name/display_id '%s'," % key,
db_rec = db.lookup(name=key)
compare_record(record, db_rec)
db_rec = db.lookup(display_id=key)
compare_record(record, db_rec)
print "OK"
key = record.id
if key.count(".")==1 and key.split(".")[1].isdigit() :
print " - Retrieving by version '%s'," % key,
db_rec = db.lookup(version=key)
compare_record(record, db_rec)
print "OK"
if "accessions" in record.annotations :
accs = set(record.annotations["accessions"])
for key in accs :
assert key, "Blank accession in annotation %s" % repr(accs)
def get_raw_check(self, filename, format, alphabet, comp):
# Also checking the key_function here
if comp:
h = gzip.open(filename, "rb")
raw_file = h.read()
h.close()
h = gzip_open(filename, format)
id_list = [
rec.id.lower() for rec in SeqIO.parse(h, format, alphabet)
]
h.close()
else:
h = open(filename, "rb")
raw_file = h.read()
h.close()
id_list = [
rec.id.lower()
for rec in SeqIO.parse(filename, format, alphabet)
]
if format in ["sff"]:
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonParserWarning)
rec_dict = SeqIO.index(filename,
format,
alphabet,
key_function=lambda x: x.lower())
else:
rec_dict = SeqIO.index(filename,
format,
alphabet,
key_function=lambda x: x.lower())
self.assertEqual(set(id_list), set(rec_dict))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assertTrue(key in rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assertTrue(isinstance(raw, bytes),
"Didn't get bytes from %s get_raw" % format)
self.assertTrue(raw.strip())
self.assertTrue(raw in raw_file)
rec1 = rec_dict[key]
# Following isn't very elegant, but it lets me test the
# __getitem__ SFF code is working.
if format in SeqIO._BinaryFormats:
handle = BytesIO(raw)
else:
handle = StringIO(_bytes_to_string(raw))
if format == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False)
elif format == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True)
elif format == "uniprot-xml":
self.assertTrue(raw.startswith(_as_bytes("<entry ")))
self.assertTrue(raw.endswith(_as_bytes("</entry>")))
# Currently the __getitem__ method uses this
# trick too, but we hope to fix that later
raw = """<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % _bytes_to_string(raw)
handle = StringIO(raw)
rec2 = SeqIO.read(handle, format, alphabet)
else:
rec2 = SeqIO.read(handle, format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict.close()
del rec_dict
iterator = SeqIO.parse(handle=open(t_filename,"r"), format=t_format)
count = db.load(iterator)
assert count == t_count
db_count += count
#print " - Committing %i records" % count
server.commit()
iterator = SeqIO.parse(handle=open(t_filename,"r"), format=t_format)
for record in iterator:
print " - %s, %s" % (checksum_summary(record), record.id)
key = record.name
print " - Retrieving by name/display_id '%s'," % key,
db_rec = db.lookup(name=key)
compare_record(record, db_rec)
db_rec = db.lookup(display_id=key)
compare_record(record, db_rec)
print "OK"
key = record.id
if key.count(".")==1 and key.split(".")[1].isdigit():
print " - Retrieving by version '%s'," % key,
db_rec = db.lookup(version=key)
compare_record(record, db_rec)
print "OK"
if "accessions" in record.annotations:
accs = sorted(set(record.annotations["accessions"]))
for key in accs:
assert key, "Blank accession in annotation %s" % repr(accs)
def get_raw_check(self, filename, format, alphabet, comp):
# Also checking the key_function here
if comp:
h = gzip.open(filename, "rb")
raw_file = h.read()
h.close()
h = gzip_open(filename, format)
id_list = [rec.id.lower() for rec in
SeqIO.parse(h, format, alphabet)]
h.close()
else:
h = open(filename, "rb")
raw_file = h.read()
h.close()
id_list = [rec.id.lower() for rec in
SeqIO.parse(filename, format, alphabet)]
if format in ["sff"]:
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonParserWarning)
rec_dict = SeqIO.index(filename, format, alphabet,
key_function=lambda x: x.lower())
rec_dict_db = SeqIO.index_db(":memory:", filename, format, alphabet,
key_function=lambda x: x.lower())
else:
rec_dict = SeqIO.index(filename, format, alphabet,
key_function=lambda x: x.lower())
rec_dict_db = SeqIO.index_db(":memory:", filename, format, alphabet,
key_function=lambda x: x.lower())
self.assertEqual(set(id_list), set(rec_dict))
self.assertEqual(set(id_list), set(rec_dict_db))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assertIn(key, rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assertTrue(isinstance(raw, bytes),
"Didn't get bytes from %s get_raw" % format)
self.assertTrue(raw.strip())
self.assertIn(raw, raw_file)
raw_db = rec_dict_db.get_raw(key)
# Via index using format-specific get_raw which scans the file,
# Via index_db in general using raw length found when indexing.
self.assertEqual(raw, raw_db,
"index and index_db .get_raw() different for %s" % format)
rec1 = rec_dict[key]
# Following isn't very elegant, but it lets me test the
# __getitem__ SFF code is working.
if format in SeqIO._BinaryFormats:
handle = BytesIO(raw)
else:
handle = StringIO(_bytes_to_string(raw))
if format == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False)
elif format == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True)
elif format == "uniprot-xml":
self.assertTrue(raw.startswith(b"<entry "))
self.assertTrue(raw.endswith(b"</entry>"))
# Currently the __getitem__ method uses this
# trick too, but we hope to fix that later
raw = """<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % _bytes_to_string(raw)
handle = StringIO(raw)
rec2 = SeqIO.read(handle, format, alphabet)
else:
rec2 = SeqIO.read(handle, format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict.close()
del rec_dict
def test_records_end(self):
recs = {}
recs[0] = SeqRecord(Seq("TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={"start": 3021494,
"srcSize": 129993255,
"strand": 1,
"size": 42})
recs[1] = SeqRecord(Seq("TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="ponAbe2.chr6",
name="ponAbe2.chr6",
description="",
annotations={"start": 16173516,
"srcSize": 174210431,
"strand": -1,
"size": 46})
recs[2] = SeqRecord(Seq("TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="panTro2.chr6",
name="panTro2.chr6",
description="",
annotations={"start": 16393864,
"srcSize": 173908612,
"strand": -1,
"size": 46})
recs[3] = SeqRecord(Seq("TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="hg18.chr6",
name="hg18.chr6",
description="",
annotations={"start": 15875298,
"srcSize": 170899992,
"strand": -1,
"size": 46})
recs[4] = SeqRecord(Seq("TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT"),
id="canFam2.chr1",
name="canFam2.chr1",
description="",
annotations={"start": 78072287,
"srcSize": 125616256,
"strand": -1,
"size": 46})
recs[5] = SeqRecord(Seq("TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----"),
id="ornAna1.chr2",
name="ornAna1.chr2",
description="",
annotations={"start": 14757144,
"srcSize": 54797317,
"strand": -1,
"size": 36})
fetched_recs = self.idx._get_record(99228)
for i in range(6):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
def test_records_end(self):
recs = {}
recs[0] = SeqRecord(
Seq("TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={
"start": 3021494,
"srcSize": 129993255,
"strand": 1,
"size": 42
})
recs[1] = SeqRecord(
Seq("TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="ponAbe2.chr6",
name="ponAbe2.chr6",
description="",
annotations={
"start": 16173516,
"srcSize": 174210431,
"strand": -1,
"size": 46
})
recs[2] = SeqRecord(
Seq("TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="panTro2.chr6",
name="panTro2.chr6",
description="",
annotations={
"start": 16393864,
"srcSize": 173908612,
"strand": -1,
"size": 46
})
recs[3] = SeqRecord(
Seq("TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="hg18.chr6",
name="hg18.chr6",
description="",
annotations={
"start": 15875298,
"srcSize": 170899992,
"strand": -1,
"size": 46
})
recs[4] = SeqRecord(
Seq("TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT"),
id="canFam2.chr1",
name="canFam2.chr1",
description="",
annotations={
"start": 78072287,
"srcSize": 125616256,
"strand": -1,
"size": 46
})
recs[5] = SeqRecord(
Seq("TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----"),
id="ornAna1.chr2",
name="ornAna1.chr2",
description="",
annotations={
"start": 14757144,
"srcSize": 54797317,
"strand": -1,
"size": 36
})
fetched_recs = self.idx._get_record(99228)
for i in range(6):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
iterator = SeqIO.parse(handle=open(t_filename, "r"), format=t_format)
count = db.load(iterator)
assert count == t_count
db_count += count
#print " - Committing %i records" % count
server.commit()
iterator = SeqIO.parse(handle=open(t_filename, "r"), format=t_format)
for record in iterator:
print " - %s, %s" % (checksum_summary(record), record.id)
key = record.name
print " - Retrieving by name/display_id '%s'," % key,
db_rec = db.lookup(name=key)
compare_record(record, db_rec)
db_rec = db.lookup(display_id=key)
compare_record(record, db_rec)
print "OK"
key = record.id
if key.count(".") == 1 and key.split(".")[1].isdigit():
print " - Retrieving by version '%s'," % key,
db_rec = db.lookup(version=key)
compare_record(record, db_rec)
print "OK"
if "accessions" in record.annotations:
accs = set(record.annotations["accessions"])
for key in accs:
assert key, "Blank accession in annotation %s" % repr(accs)
iterator = SeqIO.parse(handle=open(t_filename,"r"), format=t_format)
count = db.load(iterator)
assert count == t_count
#print " - Committing %i records" % count
server.commit()
iterator = SeqIO.parse(handle=open(t_filename,"r"), format=t_format)
for record in iterator :
print " - %s, %s" % (checksum_summary(record), record.id)
key = record.name
print " - Retrieving by name/display_id '%s'," % key,
db_rec = db.lookup(name=key)
compare_record(record, db_rec)
db_rec = db.lookup(display_id=key)
compare_record(record, db_rec)
print "OK"
key = record.id
if key.count(".")==1 and key.split(".")[1].isdigit() :
print " - Retrieving by version '%s'," % key,
db_rec = db.lookup(version=key)
compare_record(record, db_rec)
print "OK"
if "accessions" in record.annotations :
accs = set(record.annotations["accessions"])
for key in accs :
assert key, "Blank accession in annotation %s" % repr(accs)
def get_raw_check(self, filename, format, alphabet, comp):
# Also checking the key_function here
if comp:
with gzip.open(filename, "rb") as handle:
raw_file = handle.read()
with gzip_open(filename, format) as handle:
id_list = [
rec.id.lower()
for rec in SeqIO.parse(handle, format, alphabet)
]
else:
with open(filename, "rb") as handle:
raw_file = handle.read()
id_list = [
rec.id.lower()
for rec in SeqIO.parse(filename, format, alphabet)
]
if format in ["sff"]:
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonParserWarning)
rec_dict = SeqIO.index(
filename,
format,
alphabet,
key_function=lambda x: x.lower()) # noqa: E731
if sqlite3:
rec_dict_db = SeqIO.index_db(
":memory:",
filename,
format,
alphabet,
key_function=lambda x: x.lower()) # noqa: E731
else:
rec_dict = SeqIO.index(
filename, format, alphabet,
key_function=lambda x: x.lower()) # noqa: E731
if sqlite3:
rec_dict_db = SeqIO.index_db(
":memory:",
filename,
format,
alphabet,
key_function=lambda x: x.lower()) # noqa: E731
self.assertEqual(set(id_list), set(rec_dict))
if sqlite3:
self.assertEqual(set(id_list), set(rec_dict_db))
self.assertEqual(len(id_list), len(rec_dict))
for key in id_list:
self.assertIn(key, rec_dict)
self.assertEqual(key, rec_dict[key].id.lower())
self.assertEqual(key, rec_dict.get(key).id.lower())
raw = rec_dict.get_raw(key)
self.assertTrue(isinstance(raw, bytes),
"Didn't get bytes from %s get_raw" % format)
self.assertTrue(raw.strip())
self.assertIn(raw, raw_file)
if sqlite3:
raw_db = rec_dict_db.get_raw(key)
# Via index using format-specific get_raw which scans the file,
# Via index_db in general using raw length found when indexing.
self.assertEqual(
raw, raw_db,
"index and index_db .get_raw() different for %s" % format)
rec1 = rec_dict[key]
# Following isn't very elegant, but it lets me test the
# __getitem__ SFF code is working.
if format in SeqIO._BinaryFormats:
handle = BytesIO(raw)
else:
handle = StringIO(raw.decode())
if format == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=False)
elif format == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
rec_dict._proxy._alphabet,
trim=True)
elif format == "uniprot-xml":
self.assertTrue(raw.startswith(b"<entry "))
self.assertTrue(raw.endswith(b"</entry>"))
# Currently the __getitem__ method uses this
# trick too, but we hope to fix that later
raw = """<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % raw.decode()
handle = StringIO(raw)
rec2 = SeqIO.read(handle, format, alphabet)
else:
rec2 = SeqIO.read(handle, format, alphabet)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict.close()
del rec_dict
def get_raw_check(self, filename, fmt, comp):
# Also checking the key_function here
msg = "Test failure parsing file %s with format %s" % (filename, fmt)
if comp:
with gzip.open(filename, "rb") as handle:
raw_file = handle.read()
mode = "r" + self.get_mode(fmt)
with gzip.open(filename, mode) as handle:
id_list = [rec.id.lower() for rec in SeqIO.parse(handle, fmt)]
else:
with open(filename, "rb") as handle:
raw_file = handle.read()
id_list = [rec.id.lower() for rec in SeqIO.parse(filename, fmt)]
if fmt in ["sff"]:
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonParserWarning)
rec_dict = SeqIO.index(filename, fmt, key_function=str.lower)
if sqlite3:
rec_dict_db = SeqIO.index_db(
":memory:",
filename,
fmt,
key_function=str.lower,
)
else:
rec_dict = SeqIO.index(filename, fmt, key_function=str.lower)
if sqlite3:
rec_dict_db = SeqIO.index_db(
":memory:",
filename,
fmt,
key_function=str.lower,
)
self.assertEqual(set(id_list), set(rec_dict), msg=msg)
if sqlite3:
self.assertEqual(set(id_list), set(rec_dict_db), msg=msg)
self.assertEqual(len(id_list), len(rec_dict), msg=msg)
for key in id_list:
self.assertIn(key, rec_dict, msg=msg)
self.assertEqual(key, rec_dict[key].id.lower(), msg=msg)
self.assertEqual(key, rec_dict.get(key).id.lower(), msg=msg)
raw = rec_dict.get_raw(key)
self.assertIsInstance(raw, bytes, msg=msg)
self.assertTrue(raw.strip(), msg=msg)
self.assertIn(raw, raw_file, msg=msg)
if sqlite3:
raw_db = rec_dict_db.get_raw(key)
# Via index using format-specific get_raw which scans the file,
# Via index_db in general using raw length found when indexing.
self.assertEqual(raw, raw_db, msg=msg)
rec1 = rec_dict[key]
# Following isn't very elegant, but it lets me test the
# __getitem__ SFF code is working.
mode = self.get_mode(fmt)
if mode == "b":
handle = BytesIO(raw)
elif mode == "t":
handle = StringIO(raw.decode())
else:
raise RuntimeError("Unexpected mode %s" % mode)
if fmt == "sff":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
trim=False,
)
elif fmt == "sff-trim":
rec2 = SeqIO.SffIO._sff_read_seq_record(
handle,
rec_dict._proxy._flows_per_read,
rec_dict._proxy._flow_chars,
rec_dict._proxy._key_sequence,
trim=True,
)
elif fmt == "uniprot-xml":
self.assertTrue(raw.startswith(b"<entry "), msg=msg)
self.assertTrue(raw.endswith(b"</entry>"), msg=msg)
# Currently the __getitem__ method uses this
# trick too, but we hope to fix that later
raw = ("""<?xml version='1.0' encoding='UTF-8'?>
<uniprot xmlns="http://uniprot.org/uniprot"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://uniprot.org/uniprot
http://www.uniprot.org/support/docs/uniprot.xsd">
%s
</uniprot>
""" % raw.decode())
handle = StringIO(raw)
rec2 = SeqIO.read(handle, fmt)
else:
rec2 = SeqIO.read(handle, fmt)
self.assertEqual(True, compare_record(rec1, rec2))
rec_dict.close()
del rec_dict
