def test_save_and_load(self):
states = "NR"
alphabet = "AGTC"
p_initial = array([1.0, 0.0])
p_transition = array([[0.75, 0.25], [0.25, 0.75]])
p_emission = array(
[[0.45, 0.36, 0.06, 0.13], [0.24, 0.18, 0.12, 0.46]])
markov_model_save = MarkovModel.MarkovModel(
states,
alphabet,
p_initial,
p_transition,
p_emission)
handle = StringIO()
MarkovModel.save(markov_model_save, handle)
handle.seek(0)
markov_model_load = MarkovModel.load(handle)
self.assertEqual(''.join(markov_model_load.states), states)
self.assertEqual(''.join(markov_model_load.alphabet), alphabet)
self.assertTrue(array_equal(markov_model_load.p_initial, p_initial))
self.assertTrue(array_equal
(markov_model_load.p_transition, p_transition))
self.assertTrue(array_equal(markov_model_load.p_emission, p_emission))
def test_write_species(self):
"""Test writing species from annotation tags."""
record = SeqIO.read("SwissProt/sp016", "swiss")
self.assertEqual(record.annotations["organism"], "H**o sapiens (Human)")
self.assertEqual(record.annotations["ncbi_taxid"], ["9606"])
handle = StringIO()
SeqIO.write(record, handle, "seqxml")
handle.seek(0)
output = handle.getvalue()
self.assertTrue("H**o sapiens (Human)" in output)
self.assertTrue("9606" in output)
if '<species name="H**o sapiens (Human)" ncbiTaxID="9606"/>' in output:
# Good, but don't get this (do we?)
pass
elif '<species name="H**o sapiens (Human)" ncbiTaxID="9606"></species>' in output:
# Not as concise, but fine (seen on C Python)
pass
elif '<species ncbiTaxID="9606" name="H**o sapiens (Human)"></species>' in output:
# Jython uses a different order
pass
elif '<species ncbiTaxID="9606" name="H**o sapiens (Human)"/>' in output:
# This would be fine too, but don't get this (do we?)
pass
else:
raise ValueError("Mising expected <species> tag: %r" % output)
def do_comparison(good_record, test_record):
"""Compare two records to see if they are the same.
Ths compares the two GenBank record, and will raise an AssertionError
if two lines do not match, showing the non-matching lines.
"""
good_handle = StringIO(good_record)
test_handle = StringIO(test_record)
while True:
good_line = good_handle.readline()
test_line = test_handle.readline()
if not (good_line) and not (test_line):
break
if not (good_line):
raise AssertionError("Extra info in Test: %r" % test_line)
if not (test_line):
raise AssertionError("Extra info in Expected: %r" % good_line)
test_normalized = " ".join(x for x in test_line.split() if x)
good_normalized = " ".join(x for x in good_line.split() if x)
assert test_normalized == good_normalized, "Expected does not match Test.\nExpect: %r\nTest: %r\n" % (
good_line,
test_line,
)
def test_000_write_invalid_but_parsed_locus_line(self):
"""Make sure we survive writing slightly invalid LOCUS lines we could parse."""
# grab a valid file
with open(path.join('GenBank', 'NC_005816.gb'), 'r') as handle:
lines = handle.readlines()
# futz with the molecule type to make it lower case
invalid_line = "LOCUS NC_005816 9609 bp dna circular BCT 21-JUL-2008\n"
lines[0] = invalid_line
fake_handle = StringIO("".join(lines))
# Make sure parsing this actually raises a warning
with warnings.catch_warnings(record=True) as caught:
warnings.simplefilter("always")
rec = SeqIO.read(fake_handle, 'genbank')
self.assertEqual(len(caught), 1)
self.assertEqual(caught[0].category, BiopythonParserWarning)
self.assertEqual(str(caught[0].message), "Non-upper case molecule type in LOCUS line: dna")
out_handle = StringIO()
ret = SeqIO.write([rec], out_handle, 'genbank')
self.assertEqual(ret, 1)
out_handle.seek(0)
out_lines = out_handle.readlines()
self.assertEqual(out_lines[0], invalid_line)
def test_fasta_out(self):
"""Check FASTQ to FASTA output"""
records = SeqIO.parse("Quality/example.fastq", "fastq")
h = StringIO()
SeqIO.write(records, h, "fasta")
with open("Quality/example.fasta") as expected:
self.assertEqual(h.getvalue(), expected.read())
def test_widget(self):
"""Try widget derived functionality.
"""
test_widget = BasicChromosome.ChromosomeSegment()
expected_string = "chr_percent = 0.25"
# trick to write the properties to a string
save_stdout = sys.stdout
new_stdout = StringIO()
sys.stdout = new_stdout
test_widget.dumpProperties()
properties = new_stdout.getvalue()
sys.stdout = save_stdout
self.assertTrue(expected_string in properties,
"Unexpected results from dumpProperties: \n %s" % properties)
properties = test_widget.getProperties()
self.assertEqual(properties["label_size"], 6,
"Unexpected results from getProperties: %s" % properties)
test_widget.setProperties({"start_x_position": 12})
self.assertEqual(test_widget.start_x_position, 12,
"setProperties doesn't seem to work right: %s"
% test_widget.start_x_position)
def test_qual_negative(self):
"""Check QUAL negative scores mapped to PHRED zero"""
data = """>1117_10_107_F3
23 31 -1 -1 -1 29 -1 -1 20 32 -1 18 25 7 -1 6 -1 -1 -1 30 -1 20 13 7 -1 -1 21 30 -1 24 -1 22 -1 -1 22 14 -1 12 26 21 -1 5 -1 -1 -1 20 -1 -1 12 28
>1117_10_146_F3
20 33 -1 -1 -1 29 -1 -1 28 28 -1 7 16 5 -1 30 -1 -1 -1 14 -1 4 13 4 -1 -1 11 13 -1 5 -1 7 -1 -1 10 16 -1 4 12 15 -1 8 -1 -1 -1 16 -1 -1 10 4
>1117_10_1017_F3
33 33 -1 -1 -1 27 -1 -1 17 16 -1 28 24 11 -1 6 -1 -1 -1 29 -1 8 29 24 -1 -1 8 8 -1 20 -1 13 -1 -1 8 13 -1 28 10 24 -1 10 -1 -1 -1 4 -1 -1 7 6
>1117_11_136_F3
16 22 -1 -1 -1 33 -1 -1 30 27 -1 27 28 32 -1 29 -1 -1 -1 27 -1 18 9 6 -1 -1 23 16 -1 26 -1 5 7 -1 22 7 -1 18 14 8 -1 8 -1 -1 -1 11 -1 -1 4 24"""
h = StringIO(data)
h2 = StringIO()
self.assertEqual(4, SeqIO.convert(h, "qual", h2, "fastq"))
self.assertEqual(h2.getvalue(), """@1117_10_107_F3
??????????????????????????????????????????????????
+
8@!!!>!!5A!3:(!'!!!?!5.(!!6?!9!7!!7/!-;6!&!!!5!!-=
@1117_10_146_F3
??????????????????????????????????????????????????
+
5B!!!>!!==!(1&!?!!!/!%.%!!,.!&!(!!+1!%-0!)!!!1!!+%
@1117_10_1017_F3
??????????????????????????????????????????????????
+
BB!!!<!!21!=9,!'!!!>!)>9!!))!5!.!!).!=+9!+!!!%!!('
@1117_11_136_F3
??????????????????????????????????????????????????
+
17!!!B!!?<!<=A!>!!!<!3*'!!81!;!&(!7(!3/)!)!!!,!!%9
""")
def test_fastq_2000(self):
"""Read and write back simple example with upper case 2000bp read"""
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here", "ACGT"*500, "!@a~"*500)
handle = StringIO()
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
def test_fastq_1000(self):
"""Read and write back simple example with mixed case 1000bp read"""
data = "@%s\n%s\n+\n%s\n" \
% ("id descr goes here", "ACGTNncgta"*100, "abcd!!efgh"*100)
handle = StringIO()
self.assertEqual(1, SeqIO.write(SeqIO.parse(StringIO(data), "fastq"), handle, "fastq"))
self.assertEqual(data, handle.getvalue())
def test_generated(self):
"""Write and read back odd SeqRecord objects"""
record1 = SeqRecord(Seq("ACGT"*500, generic_dna), id="Test", description="Long "*500,
letter_annotations={"phred_quality":[40,30,20,10]*500})
record2 = SeqRecord(MutableSeq("NGGC"*1000), id="Mut", description="very "*1000+"long",
letter_annotations={"phred_quality":[0,5,5,10]*1000})
record3 = SeqRecord(UnknownSeq(2000,character="N"), id="Unk", description="l"+("o"*1000)+"ng",
letter_annotations={"phred_quality":[0,1]*1000})
record4 = SeqRecord(Seq("ACGT"*500), id="no_descr", description="", name="",
letter_annotations={"phred_quality":[40,50,60,62]*500})
record5 = SeqRecord(Seq("",generic_dna), id="empty_p", description="(could have been trimmed lots)",
letter_annotations={"phred_quality":[]})
record6 = SeqRecord(Seq(""), id="empty_s", description="(could have been trimmed lots)",
letter_annotations={"solexa_quality":[]})
record7 = SeqRecord(Seq("ACNN"*500), id="Test_Sol", description="Long "*500,
letter_annotations={"solexa_quality":[40,30,0,-5]*500})
record8 = SeqRecord(Seq("ACGT"), id="HighQual", description="With very large qualities that even Sanger FASTQ can't hold!",
letter_annotations={"solexa_quality":[0,10,100,1000]})
#TODO - Record with no identifier?
records = [record1, record2, record3, record4, record5, record6, record7, record8]
#TODO - Have a Biopython defined "DataLossWarning?"
warnings.simplefilter('ignore', BiopythonWarning)
#TODO - Include phd output?
for format in ["fasta", "fastq", "fastq-solexa", "fastq-illumina", "qual"]:
handle = StringIO()
SeqIO.write(records, handle, format)
handle.seek(0)
compare_records(records,
list(SeqIO.parse(handle, format)),
truncation_expected(format))
warnings.filters.pop()
def check_convert_fails(in_filename, in_format, out_format, alphabet=None):
qual_truncate = truncation_expected(out_format)
#We want the SAME error message from parse/write as convert!
err1 = None
try:
records = list(SeqIO.parse(in_filename,in_format, alphabet))
handle = StringIO()
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.write(records, handle, out_format)
if qual_truncate:
warnings.filters.pop()
handle.seek(0)
assert False, "Parse or write should have failed!"
except ValueError as err:
err1 = err
#Now do the conversion...
try:
handle2 = StringIO()
if qual_truncate:
warnings.simplefilter('ignore', UserWarning)
SeqIO.convert(in_filename, in_format, handle2, out_format, alphabet)
if qual_truncate:
warnings.filters.pop()
assert False, "Convert should have failed!"
except ValueError as err2:
assert str(err1) == str(err2), \
"Different failures, parse/write:\n%s\nconvert:\n%s" \
% (err1, err2)
def test_longer_locus_line(self):
"""Check that we can read and write files with longer locus lines."""
# Create example file from existing file
with open(path.join("GenBank", "DS830848.gb"), 'r') as inhandle:
data = inhandle.readlines()
data[0] = "LOCUS AZZZAA021234567891234 2147483647 bp DNA linear PRI 15-OCT-2018\n"
# Create memory file from modified genbank file
in_tmp = StringIO()
in_tmp.writelines(data)
in_tmp.seek(0)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
in_tmp.seek(0)
record = SeqIO.read(in_tmp, 'genbank')
# Create temporary output memory file
out_tmp = StringIO()
SeqIO.write(record, out_tmp, 'genbank')
# Check that the written file can be read back in
out_tmp.seek(0)
record_in = SeqIO.read(out_tmp, 'genbank')
self.assertEqual(record_in.id, "DS830848.1")
self.assertEqual(record_in.name, "AZZZAA021234567891234")
self.assertEqual(len(record_in.seq), 2147483647)
def test_draw_ascii(self):
"""Tree to Graph conversion."""
handle = StringIO()
tree = Phylo.read(EX_APAF, 'phyloxml')
Phylo.draw_ascii(tree, file=handle)
Phylo.draw_ascii(tree, file=handle, column_width=120)
handle.close()
def simple_check(self, base_name, in_variant):
for out_variant in ["sanger", "solexa", "illumina"]:
in_filename = "Quality/%s_original_%s.fastq" \
% (base_name, in_variant)
self.assertTrue(os.path.isfile(in_filename))
# Load the reference output...
with open("Quality/%s_as_%s.fastq" % (base_name, out_variant),
_universal_read_mode) as handle:
expected = handle.read()
with warnings.catch_warnings():
if out_variant != "sanger":
# Ignore data loss warnings from max qualities
warnings.simplefilter("ignore", BiopythonWarning)
warnings.simplefilter("ignore", UserWarning)
# Check matches using convert...
handle = StringIO()
SeqIO.convert(in_filename, "fastq-"+in_variant,
handle, "fastq-"+out_variant)
self.assertEqual(expected, handle.getvalue())
# Check matches using parse/write
handle = StringIO()
SeqIO.write(SeqIO.parse(in_filename, "fastq-"+in_variant),
handle, "fastq-"+out_variant)
self.assertEqual(expected, handle.getvalue())
def __str__(self):
"""Create a string representation of the MarkovModel object."""
from Bio._py3k import StringIO
handle = StringIO()
save(self, handle)
handle.seek(0)
return handle.read()
def loop(self, filename, format):
original_records = list(SeqIO.parse(filename, 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
handle.close()
server.close()
def test_save(self):
trieobj = trie.trie()
trieobj["foo"] = 1
k = trieobj.keys()
self.assertEqual(k, ["foo"])
v = trieobj.values()
self.assertEqual(v, [1])
self.assertEqual(trieobj.get("bar", 99), 99)
trieobj["hello"] = "55a"
self.assertEqual(trieobj.get_approximate("foo", 0), [("foo", 1, 0)])
self.assertEqual(trieobj.get_approximate("foo", 1), [("foo", 1, 0)])
self.assertEqual(trieobj.get_approximate("foa", 0), [])
self.assertEqual(trieobj.get_approximate("foa", 1), [("foo", 1, 1)])
x = sorted(trieobj.get_approximate("foa", 2))
self.assertEqual(x, [("foo", 1, 1), ("foo", 1, 2), ("foo", 1, 2)])
# foo foo- foo-
# foa f-oa fo-a
# mismatch a->o
# insertion after f, deletion of o
# insertion after o, deletion of o
x = trieobj.get_approximate("foo", 4)
y = {}
for z in x:
y[z] = y.get(z, 0) + 1
x = sorted(y.items())
self.assertEqual(x, [(("foo", 1, 0), 1), (("hello", "55a", 4), 6)])
h = StringIO()
trie.save(h, trieobj)
h.seek(0)
trieobj = trie.load(h)
k = trieobj.keys()
self.assertTrue("foo" in k)
self.assertTrue("hello" in k)
self.assertEqual(repr(trieobj["foo"]), "1")
self.assertEqual(repr(trieobj["hello"]), "'55a'")
def test_write_read(self):
"""Checking write/read."""
alignments = list(ClustalIterator(StringIO(aln_example1))) + list(ClustalIterator(StringIO(aln_example2))) * 2
handle = StringIO()
self.assertEqual(3, ClustalWriter(handle).write_file(alignments))
handle.seek(0)
for i, a in enumerate(ClustalIterator(handle)):
self.assertEqual(a.get_alignment_length(), alignments[i].get_alignment_length())
def test_format_branch_length(self):
"""Custom format string for Newick branch length serialization."""
tree = Phylo.read(StringIO("A:0.1;"), "newick")
mem_file = StringIO()
Phylo.write(tree, mem_file, "newick", format_branch_length="%.0e")
# Py2.5 compat: Windows with Py2.5- represents this as 1e-001;
# on all other platforms it's 1e-01
self.assertTrue(mem_file.getvalue().strip() in ["A:1e-01;", "A:1e-001;"])
def test_format_phylip(self):
dm = DistanceMatrix(self.names, self.matrix)
handle = StringIO()
dm.format_phylip(handle)
lines = handle.getvalue().splitlines()
self.assertEqual(len(lines), len(dm) + 1)
self.assertTrue(lines[0].endswith(str(len(dm))))
for name, line in zip(self.names, lines[1:]):
self.assertTrue(line.startswith(name))
def test_no_name(self):
"""Test FASTA record with no identifier."""
handle = StringIO(">\nACGT")
record = SeqIO.read(handle, "fasta")
handle.close()
self.assertEqual(str(record.seq), "ACGT")
self.assertEqual("", record.id)
self.assertEqual("", record.name)
self.assertEqual("", record.description)
def read_longer_than_maxsize():
with open(path.join("GenBank", "DS830848.gb"), 'r') as inhandle:
data2 = inhandle.readlines()
data2[0] = "LOCUS AZZZAA02123456789 " + str(sys.maxsize + 1) + " bp DNA linear PRI 15-OCT-2018\n"
long_in_tmp = StringIO()
long_in_tmp.writelines(data2)
long_in_tmp.seek(0)
record = SeqIO.read(long_in_tmp, 'genbank')
def test_write_read_single(self):
"""Testing write/read when there is only one sequence."""
alignment = next(ClustalIterator(StringIO(aln_example1)))
# Now thae just the first row as a new alignment:
alignment = alignment[0:1]
handle = StringIO()
ClustalWriter(handle).write_file([alignment])
handle.seek(0)
for i, a in enumerate(ClustalIterator(handle)):
self.assertEqual(a.get_alignment_length(), alignment.get_alignment_length())
self.assertEqual(len(a), 1)
def test_locus_line_topogoly(self):
"""Test if chromosome topology is conserved"""
record = SeqIO.read('GenBank/DS830848.gb', 'genbank')
self.assertEqual(record.annotations['topology'], 'linear')
out_handle = StringIO()
SeqIO.write([record], out_handle, 'genbank')
first_line = out_handle.getvalue().split('\n')[0]
self.assertIn('linear', first_line)
with open('GenBank/DS830848.gb', 'r') as fh:
orig_first_line = fh.readline().strip()
self.assertEqual(first_line, orig_first_line)
def test_write(self):
correct_output_a = """graph [
directed 1
node [
id 0
label "1"
a 1
]
node [
id 1
label "2"
]
edge [
source 0
target 1
x "x"
]
edge [
source 1
target 0
label "zzzz"
]
]"""
correct_output_b = """graph [
directed 1
node [
id 0
label "2"
]
node [
id 1
label "1"
a 1
]
edge [
source 1
target 0
x "x"
]
edge [
source 0
target 1
label "zzzz"
]
]"""
out = StringIO()
writer = GmlWriter(out)
graph = DiGraph()
graph.add_node(1, {'a' : 1 })
graph.add_edge(1, 2, {'x' : 'x'})
graph.add_edge(2, 1, "zzzz")
writer.write(graph)
self.assertIn(out.getvalue(), set([correct_output_a, correct_output_b]))
def test_newick_write(self):
"""Parse a Nexus file with multiple trees."""
# Tree with internal node labels
mem_file = StringIO()
tree = Phylo.read(StringIO("(A,B,(C,D)E)F;"), "newick")
Phylo.write(tree, mem_file, "newick")
mem_file.seek(0)
tree2 = Phylo.read(mem_file, "newick")
# Sanity check
self.assertEqual(tree2.count_terminals(), 4)
# Check internal node labels were retained
internal_names = set(c.name for c in tree2.get_nonterminals() if c is not None)
self.assertEqual(internal_names, set(("E", "F")))
def test_genbank_date_datetime(self):
"""Check if datetime objects are handled correctly."""
sequence_object = Seq("ATGC", generic_dna)
record = SeqRecord(sequence_object,
id='123456789',
name='UnitTest',
description='Test case for date parsing')
record.annotations["date"] = datetime(2000, 2, 2)
handle = StringIO()
SeqIO.write(record, handle, 'genbank')
handle.seek(0)
gb = SeqIO.read(handle, "gb")
self.assertEqual(gb.annotations["date"], "02-FEB-2000")
def _write_parse_and_compare(self, read1_records):
handle = StringIO()
SeqIO.write(read1_records, handle, "seqxml")
handle.seek(0)
read2_records = list(SeqIO.parse(handle, "seqxml"))
self.assertEqual(len(read1_records), len(read2_records))
for record1, record2 in zip(read1_records, read2_records):
assert_equal_records(self, record1, record2)
def test_genbank_date_default(self):
"""Check if default date is handled correctly."""
sequence_object = Seq("ATGC", generic_dna)
# check if default value is inserted correctly
record = SeqRecord(sequence_object,
id='123456789',
name='UnitTest',
description='Test case for date parsing')
handle = StringIO()
SeqIO.write(record, handle, 'genbank')
handle.seek(0)
gb = SeqIO.read(handle, "gb")
self.assertEqual(gb.annotations["date"], "01-JAN-1980")
def test_genbank_date_correct(self):
"""Check if user provided date is inserted correctly."""
sequence_object = Seq("ATGC", generic_dna)
record = SeqRecord(sequence_object,
id='123456789',
name='UnitTest',
description='Test case for date parsing')
record.annotations["date"] = "24-DEC-2015"
handle = StringIO()
SeqIO.write(record, handle, 'genbank')
handle.seek(0)
gb = SeqIO.read(handle, "gb")
self.assertEqual(gb.annotations["date"], "24-DEC-2015")
def get(self, offset):
"""Returns SeqRecord."""
# Should be overridden for binary file formats etc:
return self._parse(StringIO(_bytes_to_string(self.get_raw(offset))))
def check_simple_write_read(alignments, indent=" "):
# print(indent+"Checking we can write and then read back these alignments")
for format in test_write_read_align_with_seq_count:
records_per_alignment = len(alignments[0])
for a in alignments:
if records_per_alignment != len(a):
records_per_alignment = None
# Can we expect this format to work?
if not records_per_alignment \
and format not in test_write_read_alignment_formats:
continue
print(indent + "Checking can write/read as '%s' format" % format)
# Going to write to a handle...
handle = StringIO()
try:
c = AlignIO.write(alignments, handle=handle, format=format)
assert c == len(alignments)
except ValueError as e:
# This is often expected to happen, for example when we try and
# write sequences of different lengths to an alignment file.
print(indent + "Failed: %s" % str(e))
# Carry on to the next format:
continue
# First, try with the seq_count
if records_per_alignment:
handle.flush()
handle.seek(0)
try:
alignments2 = list(
AlignIO.parse(handle=handle,
format=format,
seq_count=records_per_alignment))
except ValueError as e:
# This is BAD. We can't read our own output.
# I want to see the output when called from the test harness,
# run_tests.py (which can be funny about new lines on Windows)
handle.seek(0)
raise ValueError(
"%s\n\n%s\n\n%s" %
(str(e), repr(handle.read()), repr(alignments2)))
simple_alignment_comparison(alignments, alignments2, format)
if format in test_write_read_alignment_formats:
# Don't need the seq_count
handle.flush()
handle.seek(0)
try:
alignments2 = list(AlignIO.parse(handle=handle, format=format))
except ValueError as e:
# This is BAD. We can't read our own output.
# I want to see the output when called from the test harness,
# run_tests.py (which can be funny about new lines on Windows)
handle.seek(0)
raise ValueError(
"%s\n\n%s\n\n%s" %
(str(e), repr(handle.read()), repr(alignments2)))
simple_alignment_comparison(alignments, alignments2, format)
if len(alignments) > 1:
# Try writing just one Alignment (not a list)
handle = StringIO()
AlignIO.write(alignments[0:1], handle, format)
assert handle.getvalue() == alignments[0].format(format)
import os.path
import unittest
import shutil
from Bio._py3k import StringIO
import tempfile
from Bio import File
data = """This
is
a multi-line
file"""
### UndoHandle
h = File.UndoHandle(StringIO(data))
print(h.readline()) # 'This'
print(h.peekline()) # 'is'
print(h.readline()) # 'is'
h.saveline("saved")
print(h.peekline()) # 'saved'
h.saveline("another")
print(h.readline()) # 'another'
print(h.readline()) # 'saved'
# Test readlines after saveline
h.saveline("saved again")
lines = h.readlines()
print(repr(lines[0])) # 'saved again'
print(repr(lines[1])) # 'a multi-line'
def testParse(self):
f = open("./SCOP/dir.cla.scop.txt_test")
try:
cla = f.read()
f.close()
f = open("./SCOP/dir.des.scop.txt_test")
des = f.read()
f.close()
f = open("./SCOP/dir.hie.scop.txt_test")
hie = f.read()
finally:
f.close()
scop = Scop(StringIO(cla), StringIO(des), StringIO(hie))
cla_out = StringIO()
scop.write_cla(cla_out)
lines = zip(cla.rstrip().split('\n'),
cla_out.getvalue().rstrip().split('\n'))
for expected_line, line in lines:
self.assertTrue(self._compare_cla_lines(expected_line, line))
des_out = StringIO()
scop.write_des(des_out)
self.assertEqual(des_out.getvalue(), des)
hie_out = StringIO()
scop.write_hie(hie_out)
self.assertEqual(hie_out.getvalue(), hie)
domain = scop.getDomainBySid("d1hbia_")
self.assertEqual(domain.sunid, 14996)
domains = scop.getDomains()
self.assertEqual(len(domains), 14)
self.assertEqual(domains[4].sunid, 14988)
dom = scop.getNodeBySunid(-111)
self.assertEqual(dom, None)
dom = scop.getDomainBySid("no such domain")
self.assertEqual(dom, None)
asis 549 TCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGT 598
asis 311 -------------------------------------------------- 311
asis 599 GAAAGGGGGTTAATAGC 615
asis 311 ----------------- 311
#---------------------------------------
#---------------------------------------"""
from Bio._py3k import StringIO
alignments = list(EmbossIterator(StringIO(pair_example)))
assert len(alignments) == 1
assert len(alignments[0]) == 2
assert [r.id for r in alignments[0]] \
== ["IXI_234", "IXI_235"]
alignments = list(EmbossIterator(StringIO(simple_example)))
assert len(alignments) == 1
assert len(alignments[0]) == 4
assert [r.id for r in alignments[0]] \
== ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]
alignments = list(EmbossIterator(StringIO(pair_example + simple_example)))
assert len(alignments) == 2
assert len(alignments[0]) == 2
assert len(alignments[1]) == 4
def test_stringio(self):
s = StringIO()
with File.as_handle(s) as handle:
self.assertIs(s, handle)
def test_read_write_clustal(self):
"""Test the base alignment stuff."""
path = os.path.join(os.getcwd(), "Clustalw", "opuntia.aln")
alignment = AlignIO.read(path, "clustal", alphabet=Alphabet.Gapped(IUPAC.unambiguous_dna))
self.assertEqual(len(alignment), 7)
seq_record = alignment[0]
self.assertEqual(seq_record.description, "gi|6273285|gb|AF191659.1|AF191")
self.assertEqual(seq_record.seq, Seq("TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA"))
seq_record = alignment[1]
self.assertEqual(seq_record.description, "gi|6273284|gb|AF191658.1|AF191")
self.assertEqual(seq_record.seq, "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA")
seq_record = alignment[2]
self.assertEqual(seq_record.description, "gi|6273287|gb|AF191661.1|AF191")
self.assertEqual(seq_record.seq, "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA")
seq_record = alignment[3]
self.assertEqual(seq_record.description, "gi|6273286|gb|AF191660.1|AF191")
self.assertEqual(seq_record.seq, "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA")
seq_record = alignment[4]
self.assertEqual(seq_record.description, "gi|6273290|gb|AF191664.1|AF191")
self.assertEqual(seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA")
seq_record = alignment[5]
self.assertEqual(seq_record.description, "gi|6273289|gb|AF191663.1|AF191")
self.assertEqual(seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA")
seq_record = alignment[6]
self.assertEqual(seq_record.description, "gi|6273291|gb|AF191665.1|AF191")
self.assertEqual(seq_record.seq, "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA")
self.assertEqual(alignment.get_alignment_length(), 156)
align_info = AlignInfo.SummaryInfo(alignment)
consensus = align_info.dumb_consensus()
self.assertIsInstance(consensus, Seq)
self.assertEqual(consensus, "TATACATTAAAGXAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTXCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA")
dictionary = align_info.replacement_dictionary(["N"])
self.assertEqual(len(dictionary), 16)
self.assertAlmostEqual(dictionary[("A", "A")], 1395.0, places=1)
self.assertAlmostEqual(dictionary[("A", "C")], 3.0, places=1)
self.assertAlmostEqual(dictionary[("A", "G")], 13.0, places=1)
self.assertAlmostEqual(dictionary[("A", "T")], 6.0, places=1)
self.assertAlmostEqual(dictionary[("C", "A")], 3.0, places=1)
self.assertAlmostEqual(dictionary[("C", "C")], 271.0, places=1)
self.assertAlmostEqual(dictionary[("C", "G")], 0, places=1)
self.assertAlmostEqual(dictionary[("C", "T")], 16.0, places=1)
self.assertAlmostEqual(dictionary[("G", "A")], 5.0, places=1)
self.assertAlmostEqual(dictionary[("G", "C")], 0, places=1)
self.assertAlmostEqual(dictionary[("G", "G")], 480.0, places=1)
self.assertAlmostEqual(dictionary[("G", "T")], 0, places=1)
self.assertAlmostEqual(dictionary[("T", "A")], 6.0, places=1)
self.assertAlmostEqual(dictionary[("T", "C")], 12.0, places=1)
self.assertAlmostEqual(dictionary[("T", "G")], 0, places=1)
self.assertAlmostEqual(dictionary[("T", "T")], 874.0, places=1)
matrix = align_info.pos_specific_score_matrix(consensus, ["N"])
self.assertEqual(str(matrix), """\
A C G T
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 1.0 0.0 0.0 6.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
X 4.0 0.0 3.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
C 0.0 7.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
C 0.0 7.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 4.0
A 4.0 0.0 0.0 0.0
T 0.0 0.0 0.0 3.0
A 3.0 0.0 0.0 0.0
T 0.0 0.0 0.0 1.0
A 1.0 0.0 0.0 0.0
T 0.0 0.0 0.0 1.0
A 1.0 0.0 0.0 0.0
T 0.0 0.0 0.0 1.0
A 1.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
C 1.0 6.0 0.0 0.0
A 6.0 0.0 0.0 1.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
X 0.0 3.0 0.0 4.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 2.0 0.0 5.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
T 0.0 1.0 0.0 6.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
T 0.0 0.0 0.0 7.0
G 1.0 0.0 6.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
""")
matrix = align_info.pos_specific_score_matrix(chars_to_ignore=["N"])
self.assertEqual(str(matrix), """\
A C G T
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 1.0 0.0 0.0 6.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
X 4.0 0.0 3.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
C 0.0 7.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
C 0.0 7.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 4.0
A 4.0 0.0 0.0 0.0
T 0.0 0.0 0.0 3.0
A 3.0 0.0 0.0 0.0
T 0.0 0.0 0.0 1.0
A 1.0 0.0 0.0 0.0
T 0.0 0.0 0.0 1.0
A 1.0 0.0 0.0 0.0
T 0.0 0.0 0.0 1.0
A 1.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
C 1.0 6.0 0.0 0.0
A 6.0 0.0 0.0 1.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
X 0.0 3.0 0.0 4.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 2.0 0.0 5.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
T 0.0 1.0 0.0 6.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
T 0.0 0.0 0.0 7.0
G 1.0 0.0 6.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
""")
second_seq = alignment[1].seq
matrix = align_info.pos_specific_score_matrix(second_seq, ["N"])
self.assertEqual(str(matrix), """\
A C G T
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 1.0 0.0 0.0 6.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 4.0 0.0 3.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
C 0.0 7.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
G 0.0 0.0 7.0 0.0
C 0.0 7.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 4.0
A 4.0 0.0 0.0 0.0
- 0.0 0.0 0.0 3.0
- 3.0 0.0 0.0 0.0
- 0.0 0.0 0.0 1.0
- 1.0 0.0 0.0 0.0
- 0.0 0.0 0.0 1.0
- 1.0 0.0 0.0 0.0
- 0.0 0.0 0.0 1.0
- 1.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
C 1.0 6.0 0.0 0.0
A 6.0 0.0 0.0 1.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
T 0.0 3.0 0.0 4.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
C 0.0 2.0 0.0 5.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
C 0.0 7.0 0.0 0.0
T 0.0 1.0 0.0 6.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
T 0.0 0.0 0.0 7.0
G 1.0 0.0 6.0 0.0
T 0.0 0.0 0.0 7.0
A 7.0 0.0 0.0 0.0
C 0.0 7.0 0.0 0.0
C 0.0 7.0 0.0 0.0
A 7.0 0.0 0.0 0.0
G 0.0 0.0 7.0 0.0
A 7.0 0.0 0.0 0.0
""")
value = align_info.information_content(5, 50, chars_to_ignore=["N"])
self.assertAlmostEqual(value, 88.42, places=2)
value = align_info.information_content(chars_to_ignore=["N"])
self.assertAlmostEqual(value, 287.55, places=2)
e_freq = {"G": 0.25, "C": 0.25, "A": 0.25, "T": 0.25}
e_freq_table = FreqTable.FreqTable(e_freq, FreqTable.FREQ,
IUPAC.unambiguous_dna)
value = align_info.information_content(e_freq_table=e_freq_table,
chars_to_ignore=["N"])
self.assertAlmostEqual(value, 287.55, places=2)
self.assertEqual(align_info.get_column(1), "AAAAAAA")
self.assertAlmostEqual(align_info.ic_vector[1], 2.00, places=2)
self.assertEqual(align_info.get_column(7), "TTTATTT")
self.assertAlmostEqual(align_info.ic_vector[7], 1.41, places=2)
handle = StringIO()
AlignInfo.print_info_content(align_info, fout=handle)
self.assertEqual(handle.getvalue(), """\
0 T 2.000
1 A 2.000
2 T 2.000
3 A 2.000
4 C 2.000
5 A 2.000
6 T 2.000
7 T 1.408
8 A 2.000
9 A 2.000
10 A 2.000
11 G 2.000
12 A 1.015
13 A 2.000
14 G 2.000
15 G 2.000
16 G 2.000
17 G 2.000
18 G 2.000
19 A 2.000
20 T 2.000
21 G 2.000
22 C 2.000
23 G 2.000
24 G 2.000
25 A 2.000
26 T 2.000
27 A 2.000
28 A 2.000
29 A 2.000
30 T 2.000
31 G 2.000
32 G 2.000
33 A 2.000
34 A 2.000
35 A 2.000
36 G 2.000
37 G 2.000
38 C 2.000
39 G 2.000
40 A 2.000
41 A 2.000
42 A 2.000
43 G 2.000
44 A 2.000
45 A 2.000
46 A 2.000
47 G 2.000
48 A 2.000
49 A 2.000
50 T 2.000
51 A 2.000
52 T 2.000
53 A 2.000
54 T 2.000
55 A 2.000
56 - 0.682
57 - 0.682
58 - 0.333
59 - 0.333
60 - -0.115
61 - -0.115
62 - -0.115
63 - -0.115
64 - -0.115
65 - -0.115
66 A 2.000
67 T 2.000
68 A 2.000
69 T 2.000
70 A 2.000
71 T 2.000
72 T 2.000
73 T 2.000
74 C 1.408
75 A 1.408
76 A 2.000
77 A 2.000
78 T 2.000
79 T 2.000
80 T 1.015
81 C 2.000
82 C 2.000
83 T 2.000
84 T 2.000
85 A 2.000
86 T 2.000
87 A 2.000
88 T 2.000
89 A 2.000
90 C 1.137
91 C 2.000
92 C 2.000
93 A 2.000
94 A 2.000
95 A 2.000
96 T 2.000
97 A 2.000
98 T 2.000
99 A 2.000
100 A 2.000
101 A 2.000
102 A 2.000
103 A 2.000
104 T 2.000
105 A 2.000
106 T 2.000
107 C 2.000
108 T 2.000
109 A 2.000
110 A 2.000
111 T 2.000
112 A 2.000
113 A 2.000
114 A 2.000
115 T 2.000
116 T 2.000
117 A 2.000
118 G 2.000
119 A 2.000
120 T 2.000
121 G 2.000
122 A 2.000
123 A 2.000
124 T 2.000
125 A 2.000
126 T 2.000
127 C 2.000
128 A 2.000
129 A 2.000
130 A 2.000
131 G 2.000
132 A 2.000
133 A 2.000
134 T 2.000
135 C 2.000
136 C 1.408
137 A 2.000
138 T 2.000
139 T 2.000
140 G 2.000
141 A 2.000
142 T 2.000
143 T 2.000
144 T 2.000
145 A 2.000
146 G 2.000
147 T 2.000
148 G 1.408
149 T 2.000
150 A 2.000
151 C 2.000
152 C 2.000
153 A 2.000
154 G 2.000
155 A 2.000
""")
def from_string(cls, treetext):
"""Convert file handle to StringIO object."""
handle = StringIO(treetext)
return cls(handle)
def test_invalid_format(self):
"""Check convert file format checking."""
self.assertRaises(ValueError, TogoWS.convert, StringIO("PLACEHOLDER"),
"genbank", "invalid_for_testing")
self.assertRaises(ValueError, TogoWS.convert, StringIO("PLACEHOLDER"),
"invalid_for_testing", "fasta")
print(is_blank_line('', allow_spaces=1)) # 1
print(is_blank_line('', allow_spaces=0)) # 1
print(is_blank_line(string.whitespace, allow_spaces=1)) # 1
print(is_blank_line('hello')) # 0
print(is_blank_line('hello', allow_spaces=1)) # 0
print(is_blank_line('hello', allow_spaces=0)) # 0
print(is_blank_line(string.whitespace, allow_spaces=0)) # 0
### safe_readline
print("Running tests on safe_readline")
data = """This
file"""
h = File.UndoHandle(StringIO(data))
safe_readline = ParserSupport.safe_readline
print(safe_readline(h)) # "This"
print(safe_readline(h)) # "file"
try:
safe_readline(h)
except ValueError:
print("correctly failed")
else:
print("ERROR, should have failed")
### safe_peekline
print("Running tests on safe_peekline")
safe_peekline = ParserSupport.safe_peekline
def qblast(
program,
database,
sequence,
auto_format=None,
composition_based_statistics=None,
db_genetic_code=None,
endpoints=None,
entrez_query='(none)',
expect=10.0,
filter=None,
gapcosts=None,
genetic_code=None,
hitlist_size=50,
i_thresh=None,
layout=None,
lcase_mask=None,
matrix_name=None,
nucl_penalty=None,
nucl_reward=None,
other_advanced=None,
perc_ident=None,
phi_pattern=None,
query_file=None,
query_believe_defline=None,
query_from=None,
query_to=None,
searchsp_eff=None,
service=None,
threshold=None,
ungapped_alignment=None,
word_size=None,
alignments=500,
alignment_view=None,
descriptions=500,
entrez_links_new_window=None,
expect_low=None,
expect_high=None,
format_entrez_query=None,
format_object=None,
format_type='XML',
ncbi_gi=None,
results_file=None,
show_overview=None,
megablast=None,
):
"""Do a BLAST search using the QBLAST server at NCBI.
Supports all parameters of the qblast API for Put and Get.
Some useful parameters:
program blastn, blastp, blastx, tblastn, or tblastx (lower case)
database Which database to search against (e.g. "nr").
sequence The sequence to search.
ncbi_gi TRUE/FALSE whether to give 'gi' identifier.
descriptions Number of descriptions to show. Def 500.
alignments Number of alignments to show. Def 500.
expect An expect value cutoff. Def 10.0.
matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
filter "none" turns off filtering. Default no filtering
format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".
entrez_query Entrez query to limit Blast search
hitlist_size Number of hits to return. Default 50
megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
"""
import time
assert program in ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx']
# Format the "Put" command, which sends search requests to qblast.
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
# Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
# To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
# (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
parameters = [
('AUTO_FORMAT', auto_format),
('COMPOSITION_BASED_STATISTICS', composition_based_statistics),
('DATABASE', database),
('DB_GENETIC_CODE', db_genetic_code),
('ENDPOINTS', endpoints),
('ENTREZ_QUERY', entrez_query),
('EXPECT', expect),
('FILTER', filter),
('GAPCOSTS', gapcosts),
('GENETIC_CODE', genetic_code),
('HITLIST_SIZE', hitlist_size),
('I_THRESH', i_thresh),
('LAYOUT', layout),
('LCASE_MASK', lcase_mask),
('MEGABLAST', megablast),
('MATRIX_NAME', matrix_name),
('NUCL_PENALTY', nucl_penalty),
('NUCL_REWARD', nucl_reward),
('OTHER_ADVANCED', other_advanced),
('PERC_IDENT', perc_ident),
('PHI_PATTERN', phi_pattern),
('PROGRAM', program),
# ('PSSM',pssm), - It is possible to use PSI-BLAST via this API?
('QUERY', sequence),
('QUERY_FILE', query_file),
('QUERY_BELIEVE_DEFLINE', query_believe_defline),
('QUERY_FROM', query_from),
('QUERY_TO', query_to),
# ('RESULTS_FILE',...), - Can we use this parameter?
('SEARCHSP_EFF', searchsp_eff),
('SERVICE', service),
('THRESHOLD', threshold),
('UNGAPPED_ALIGNMENT', ungapped_alignment),
('WORD_SIZE', word_size),
('CMD', 'Put'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Send off the initial query to qblast.
# Note the NCBI do not currently impose a rate limit here, other
# than the request not to make say 50 queries at once using multiple
# threads.
request = _Request("http://blast.ncbi.nlm.nih.gov/Blast.cgi", message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
# Format the "Get" command, which gets the formatted results from qblast
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
rid, rtoe = _parse_qblast_ref_page(handle)
parameters = [
('ALIGNMENTS', alignments),
('ALIGNMENT_VIEW', alignment_view),
('DESCRIPTIONS', descriptions),
('ENTREZ_LINKS_NEW_WINDOW', entrez_links_new_window),
('EXPECT_LOW', expect_low),
('EXPECT_HIGH', expect_high),
('FORMAT_ENTREZ_QUERY', format_entrez_query),
('FORMAT_OBJECT', format_object),
('FORMAT_TYPE', format_type),
('NCBI_GI', ncbi_gi),
('RID', rid),
('RESULTS_FILE', results_file),
('SERVICE', service),
('SHOW_OVERVIEW', show_overview),
('CMD', 'Get'),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Poll NCBI until the results are ready. Use a backoff delay from 2 - 120 second wait
delay = 2.0
previous = time.time()
while True:
current = time.time()
wait = previous + delay - current
if wait > 0:
time.sleep(wait)
previous = current + wait
else:
previous = current
if delay + .5 * delay <= 120:
delay += .5 * delay
else:
delay = 120
request = _Request("http://blast.ncbi.nlm.nih.gov/Blast.cgi", message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
results = _as_string(handle.read())
# Can see an "\n\n" page while results are in progress,
# if so just wait a bit longer...
if results == "\n\n":
continue
# XML results don't have the Status tag when finished
if "Status=" not in results:
break
i = results.index("Status=")
j = results.index("\n", i)
status = results[i + len("Status="):j].strip()
if status.upper() == "READY":
break
return StringIO(results)
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(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
def test_pair_example3(self):
alignments = list(EmbossIterator(StringIO(pair_example3)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual([r.id for r in alignments[0]], ["asis", "asis"])
def test_simple_example(self):
alignments = list(EmbossIterator(StringIO(simple_example)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 4)
self.assertEqual([r.id for r in alignments[0]],
["IXI_234", "IXI_235", "IXI_236", "IXI_237"])
def parse_str(self, string):
return self.parse(StringIO(string))
self.xml_generator.endElement("property")
elif isinstance(value, (int, float, basestring)):
attr = {"name": key, "value": str(value)}
self.xml_generator.startElement(
"property", AttributesImpl(attr))
self.xml_generator.endElement("property")
if __name__ == "__main__":
print("Running quick self test")
from Bio import SeqIO
import sys
with open("Tests/SeqXML/protein_example.xml", "r") as fileHandle:
records = list(SeqIO.parse(fileHandle, "seqxml"))
from Bio._py3k import StringIO
stringHandle = StringIO()
SeqIO.write(records, stringHandle, "seqxml")
SeqIO.write(records, sys.stdout, "seqxml")
print("")
stringHandle.seek(0)
records = list(SeqIO.parse(stringHandle, "seqxml"))
SeqIO.write(records, sys.stdout, "seqxml")
print("")
def test_parse_qblast_ref_page(self):
with open("Blast/html_msgid_29_blastx_001.html", "r") as f:
handle = StringIO(f.read())
self.assertRaises(ValueError, NCBIWWW._parse_qblast_ref_page, handle)
def from_string(cls, treetext):
"""Instantiate the Newick Tree class from the given string."""
handle = StringIO(treetext)
return cls(handle)
def test_read(self):
"""Test read method"""
h = File.UndoHandle(StringIO("some text"))
h.saveline("more text")
self.assertEqual(h.read(), 'more textsome text')
def test_empty_file_read(self):
self.assertEqual([], list(NexusIterator(StringIO())))
def _do_segmentation(cnarr, method, threshold, variants=None,
skip_low=False, skip_outliers=10, min_weight=0,
save_dataframe=False, rlibpath=None):
"""Infer copy number segments from the given coverage table."""
if not len(cnarr):
return cnarr
filtered_cn = cnarr.copy()
# Filter out bins with no or near-zero sequencing coverage
if skip_low:
filtered_cn = filtered_cn.drop_low_coverage(verbose=False)
# Filter by distance from rolling quantiles
if skip_outliers:
filtered_cn = drop_outliers(filtered_cn, 50, skip_outliers)
# Filter by bin weights
if min_weight:
weight_too_low = (filtered_cn["weight"] < min_weight).fillna(True)
else:
weight_too_low = (filtered_cn["weight"] == 0).fillna(True)
n_weight_too_low = weight_too_low.sum() if len(weight_too_low) else 0
if n_weight_too_low:
filtered_cn = filtered_cn[~weight_too_low]
if min_weight:
logging.debug("Dropped %d bins with weight below %s",
n_weight_too_low, min_weight)
else:
logging.debug("Dropped %d bins with zero weight",
n_weight_too_low)
if len(filtered_cn) != len(cnarr):
msg = ("Dropped %d / %d bins"
% (len(cnarr) - len(filtered_cn), len(cnarr)))
if cnarr["chromosome"].iat[0] == cnarr["chromosome"].iat[-1]:
msg += " on chromosome " + str(cnarr["chromosome"].iat[0])
logging.info(msg)
if not len(filtered_cn):
return filtered_cn
seg_out = ""
if method == 'haar':
segarr = haar.segment_haar(filtered_cn, threshold)
elif method == 'none':
segarr = none.segment_none(filtered_cn)
elif method.startswith('hmm'):
segarr = hmm.segment_hmm(filtered_cn, method, threshold)
elif method in ('cbs', 'flasso'):
# Run R scripts to calculate copy number segments
rscript = {'cbs': cbs.CBS_RSCRIPT,
'flasso': flasso.FLASSO_RSCRIPT,
}[method]
filtered_cn['start'] += 1 # Convert to 1-indexed coordinates for R
with tempfile.NamedTemporaryFile(suffix='.cnr', mode="w+t") as tmp:
# TODO tabio.write(filtered_cn, tmp, 'seg')
filtered_cn.data.to_csv(tmp, index=False, sep='\t',
float_format='%.6g', mode="w+t")
tmp.flush()
script_strings = {
'probes_fname': tmp.name,
'sample_id': cnarr.sample_id,
'threshold': threshold,
'rlibpath': ('.libPaths(c("%s"))' % rlibpath if rlibpath else ''),
}
with core.temp_write_text(rscript % script_strings,
mode='w+t') as script_fname:
seg_out = core.call_quiet('~/conda/cnvkit_r/bin/Rscript', '--vanilla', script_fname)
# Convert R dataframe contents (SEG) to a proper CopyNumArray
# NB: Automatically shifts 'start' back from 1- to 0-indexed
segarr = tabio.read(StringIO(seg_out.decode()), "seg", into=CNA)
if method == 'flasso':
# Merge adjacent bins with same log2 value into segments
if 'weight' in filtered_cn:
segarr['weight'] = filtered_cn['weight']
else:
segarr['weight'] = 1.0
segarr = squash_by_groups(segarr, segarr['log2'], by_arm=True)
else:
raise ValueError("Unknown method %r" % method)
segarr.meta = cnarr.meta.copy()
if variants and not method.startswith('hmm'):
# Re-segment the variant allele freqs within each segment
newsegs = [haar.variants_in_segment(subvarr, segment, 0.01 * threshold)
for segment, subvarr in variants.by_ranges(segarr)]
segarr = segarr.as_dataframe(pd.concat(newsegs))
segarr['baf'] = variants.baf_by_ranges(segarr)
segarr = transfer_fields(segarr, cnarr)
if save_dataframe:
return segarr, seg_out
else:
return segarr
def test_write_alignment(self):
# Default causes no interleave (columns <= 1000)
records = [
SeqRecord(Seq("ATGCTGCTGA" * 90, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 90, data)
# Default causes interleave (columns > 1000)
records = [
SeqRecord(Seq("ATGCTGCTGA" * 110, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 90, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: True
records = [
SeqRecord(Seq("ATGCTGCTGA" * 9, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=True)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 9, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: False
records = [
SeqRecord(Seq("ATGCTGCTGA" * 110, alphabet=ambiguous_dna), id=_id)
for _id in ["foo", "bar", "baz"]
]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=False)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 110, data)
def qblast(
program,
database,
sequence,
url_base=NCBI_BLAST_URL,
auto_format=None,
composition_based_statistics=None,
db_genetic_code=None,
endpoints=None,
entrez_query="(none)",
expect=10.0,
filter=None,
gapcosts=None,
genetic_code=None,
hitlist_size=50,
i_thresh=None,
layout=None,
lcase_mask=None,
matrix_name=None,
nucl_penalty=None,
nucl_reward=None,
other_advanced=None,
perc_ident=None,
phi_pattern=None,
query_file=None,
query_believe_defline=None,
query_from=None,
query_to=None,
searchsp_eff=None,
service=None,
threshold=None,
ungapped_alignment=None,
word_size=None,
short_query=None,
alignments=500,
alignment_view=None,
descriptions=500,
entrez_links_new_window=None,
expect_low=None,
expect_high=None,
format_entrez_query=None,
format_object=None,
format_type="XML",
ncbi_gi=None,
results_file=None,
show_overview=None,
megablast=None,
template_type=None,
template_length=None,
):
"""BLAST search using NCBI's QBLAST server or a cloud service provider.
Supports all parameters of the old qblast API for Put and Get.
Please note that NCBI uses the new Common URL API for BLAST searches
on the internet (http://ncbi.github.io/blast-cloud/dev/api.html). Thus,
some of the parameters used by this function are not (or are no longer)
officially supported by NCBI. Although they are still functioning, this
may change in the future.
The Common URL API (http://ncbi.github.io/blast-cloud/dev/api.html) allows
doing BLAST searches on cloud servers. To use this feature, please set
``url_base='http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi'``
and ``format_object='Alignment'``. For more details, please see
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast
Some useful parameters:
- program blastn, blastp, blastx, tblastn, or tblastx (lower case)
- database Which database to search against (e.g. "nr").
- sequence The sequence to search.
- ncbi_gi TRUE/FALSE whether to give 'gi' identifier.
- descriptions Number of descriptions to show. Def 500.
- alignments Number of alignments to show. Def 500.
- expect An expect value cutoff. Def 10.0.
- matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
- filter "none" turns off filtering. Default no filtering
- format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".
- entrez_query Entrez query to limit Blast search
- hitlist_size Number of hits to return. Default 50
- megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
- short_query TRUE/FALSE whether to adjust the search parameters for a
short query sequence. Note that this will override
manually set parameters like word size and e value. Turns
off when sequence length is > 30 residues. Default: None.
- service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
https://ncbi.github.io/blast-cloud/dev/api.html
"""
import time
programs = ["blastn", "blastp", "blastx", "tblastn", "tblastx"]
if program not in programs:
raise ValueError("Program specified is %s. Expected one of %s" %
(program, ", ".join(programs)))
# SHORT_QUERY_ADJUST throws an error when using blastn (wrong parameter
# assignment from NCBIs side).
# Thus we set the (known) parameters directly:
if short_query and program == "blastn":
short_query = None
# We only use the 'short-query' parameters for short sequences:
if len(sequence) < 31:
expect = 1000
word_size = 7
nucl_reward = 1
filter = None
lcase_mask = None
warnings.warn(
'"SHORT_QUERY_ADJUST" is incorrectly implemented '
"(by NCBI) for blastn. We bypass the problem by "
"manually adjusting the search parameters. Thus, "
"results may slightly differ from web page "
"searches.", BiopythonWarning)
# Format the "Put" command, which sends search requests to qblast.
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
# Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
# To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
# (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
parameters = [
("AUTO_FORMAT", auto_format),
("COMPOSITION_BASED_STATISTICS", composition_based_statistics),
("DATABASE", database),
("DB_GENETIC_CODE", db_genetic_code),
("ENDPOINTS", endpoints),
("ENTREZ_QUERY", entrez_query),
("EXPECT", expect),
("FILTER", filter),
("GAPCOSTS", gapcosts),
("GENETIC_CODE", genetic_code),
("HITLIST_SIZE", hitlist_size),
("I_THRESH", i_thresh),
("LAYOUT", layout),
("LCASE_MASK", lcase_mask),
("MEGABLAST", megablast),
("MATRIX_NAME", matrix_name),
("NUCL_PENALTY", nucl_penalty),
("NUCL_REWARD", nucl_reward),
("OTHER_ADVANCED", other_advanced),
("PERC_IDENT", perc_ident),
("PHI_PATTERN", phi_pattern),
("PROGRAM", program),
# ('PSSM',pssm), - It is possible to use PSI-BLAST via this API?
("QUERY", sequence),
("QUERY_FILE", query_file),
("QUERY_BELIEVE_DEFLINE", query_believe_defline),
("QUERY_FROM", query_from),
("QUERY_TO", query_to),
# ('RESULTS_FILE',...), - Can we use this parameter?
("SEARCHSP_EFF", searchsp_eff),
("SERVICE", service),
("SHORT_QUERY_ADJUST", short_query),
("TEMPLATE_TYPE", template_type),
("TEMPLATE_LENGTH", template_length),
("THRESHOLD", threshold),
("UNGAPPED_ALIGNMENT", ungapped_alignment),
("WORD_SIZE", word_size),
("CMD", "Put"),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Send off the initial query to qblast.
# Note the NCBI do not currently impose a rate limit here, other
# than the request not to make say 50 queries at once using multiple
# threads.
request = _Request(url_base, message, {"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
# Format the "Get" command, which gets the formatted results from qblast
# Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
rid, rtoe = _parse_qblast_ref_page(handle)
parameters = [
("ALIGNMENTS", alignments),
("ALIGNMENT_VIEW", alignment_view),
("DESCRIPTIONS", descriptions),
("ENTREZ_LINKS_NEW_WINDOW", entrez_links_new_window),
("EXPECT_LOW", expect_low),
("EXPECT_HIGH", expect_high),
("FORMAT_ENTREZ_QUERY", format_entrez_query),
("FORMAT_OBJECT", format_object),
("FORMAT_TYPE", format_type),
("NCBI_GI", ncbi_gi),
("RID", rid),
("RESULTS_FILE", results_file),
("SERVICE", service),
("SHOW_OVERVIEW", show_overview),
("CMD", "Get"),
]
query = [x for x in parameters if x[1] is not None]
message = _as_bytes(_urlencode(query))
# Poll NCBI until the results are ready.
# https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
# 1. Do not contact the server more often than once every 10 seconds.
# 2. Do not poll for any single RID more often than once a minute.
# 3. Use the URL parameter email and tool, so that the NCBI
# can contact you if there is a problem.
# 4. Run scripts weekends or between 9 pm and 5 am Eastern time
# on weekdays if more than 50 searches will be submitted.
# --
# Could start with a 10s delay, but expect most short queries
# will take longer thus at least 70s with delay. Therefore,
# start with 20s delay, thereafter once a minute.
delay = 20 # seconds
while True:
current = time.time()
wait = qblast._previous + delay - current
if wait > 0:
time.sleep(wait)
qblast._previous = current + wait
else:
qblast._previous = current
# delay by at least 60 seconds only if running the request against the public NCBI API
if delay < 60 and url_base == NCBI_BLAST_URL:
# Wasn't a quick return, must wait at least a minute
delay = 60
request = _Request(url_base, message,
{"User-Agent": "BiopythonClient"})
handle = _urlopen(request)
results = _as_string(handle.read())
# Can see an "\n\n" page while results are in progress,
# if so just wait a bit longer...
if results == "\n\n":
continue
# XML results don't have the Status tag when finished
if "Status=" not in results:
break
i = results.index("Status=")
j = results.index("\n", i)
status = results[i + len("Status="):j].strip()
if status.upper() == "READY":
break
return StringIO(results)
def from_string(cls, treetext):
handle = StringIO(treetext)
return cls(handle)
def test_newick_read_scinot(self):
"""Parse Newick branch lengths in scientific notation."""
tree = Phylo.read(StringIO("(foo:1e-1,bar:0.1)"), 'newick')
clade_a = tree.clade[0]
self.assertEqual(clade_a.name, 'foo')
self.assertAlmostEqual(clade_a.branch_length, 0.1)
>>><<<
579 residues in 3 query sequences
45119 residues in 180 library sequences
Scomplib [34.26]
start: Tue May 20 16:38:45 2008 done: Tue May 20 16:38:45 2008
Total Scan time: 0.020 Total Display time: 0.010
Function used was FASTA [version 34.26 January 12, 2007]
"""
from Bio._py3k import StringIO
alignments = list(FastaM10Iterator(StringIO(simple_example)))
assert len(alignments) == 4, len(alignments)
assert len(alignments[0]) == 2
for a in alignments:
print("Alignment %i sequences of length %i" %
(len(a), a.get_alignment_length()))
for r in a:
print("%s %s %i" % (r.seq, r.id, r.annotations["original_length"]))
# print(a.annotations)
print("Done")
import os
path = "../../Tests/Fasta/"
files = sorted(f for f in os.listdir(path)
if os.path.splitext(f)[-1] == ".m10")
for filename in files:
def CifAtomIterator(handle):
"""Return SeqRecord objects for each chain in a PDB file.
The sequences are derived from the 3D structure (ATOM records), not the
SEQRES lines in the PDB file header.
Unrecognised three letter amino acid codes (e.g. "CSD") from HETATM entries
are converted to "X" in the sequence.
In addition to information from the PDB header (which is the same for all
records), the following chain specific information is placed in the
annotation:
record.annotations["residues"] = List of residue ID strings
record.annotations["chain"] = Chain ID (typically A, B ,...)
record.annotations["model"] = Model ID (typically zero)
Where amino acids are missing from the structure, as indicated by residue
numbering, the sequence is filled in with 'X' characters to match the size
of the missing region, and None is included as the corresponding entry in
the list record.annotations["residues"].
This function uses the Bio.PDB module to do most of the hard work. The
annotation information could be improved but this extra parsing should be
done in parse_pdb_header, not this module.
This gets called internally via Bio.SeqIO for the atom based interpretation
of the PDB file format:
>>> from Bio import SeqIO
>>> for record in SeqIO.parse("PDB/1A8O.cif", "cif-atom"):
... print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
...
Record id 1A8O:A, chain A
Equivalently,
>>> with open("PDB/1A8O.cif") as handle:
... for record in CifAtomIterator(handle):
... print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
...
Record id 1A8O:A, chain A
"""
# TODO - Add record.annotations to the doctest, esp the residues (not working?)
# Only import parser when needed, to avoid/delay NumPy dependency in SeqIO
from Bio.PDB.MMCIFParser import MMCIFParser
# The PdbAtomIterator uses UndoHandle to peek at the first line and get the
# PDB ID. The equivalent for mmCIF is the _entry.id field. AFAIK, the mmCIF
# format does not constrain the order of fields, so we need to parse the
# entire file using MMCIF2Dict. We copy the contents of the handle into a
# StringIO buffer first, so that both MMCIF2Dict and MMCIFParser can
# consume the handle.
buffer = StringIO()
shutil.copyfileobj(handle, buffer)
buffer.seek(0)
mmcif_dict = MMCIF2Dict(buffer)
if "_entry.id" in mmcif_dict:
pdb_id = mmcif_dict["_entry.id"]
if isinstance(pdb_id, list):
pdb_id = pdb_id[0]
else:
warnings.warn(
"Could not find the '_entry.id' field; can't determine "
"PDB ID.", BiopythonParserWarning)
pdb_id = '????'
buffer.seek(0)
struct = MMCIFParser().get_structure(pdb_id, buffer)
for record in AtomIterator(pdb_id, struct):
yield record
def test_phenotype_IO(self):
"""Test basic functionalities of phenotype IO methods."""
p1 = phenotype.read(SMALL_JSON_PLATE, "pm-json")
p2 = next(phenotype.parse(SMALL_CSV_PLATES, "pm-csv"))
handle = StringIO()
c = phenotype.write([p1, p2], handle, "pm-json")
self.assertEqual(c, 2)
handle.flush()
handle.seek(0)
# Now ready to read back from the handle...
try:
records = list(phenotype.parse(handle, "pm-json"))
except ValueError as e:
# This is BAD. We can't read our own output.
# I want to see the output when called from the test harness,
# run_tests.py (which can be funny about new lines on Windows)
handle.seek(0)
raise ValueError("%s\n\n%s\n\n%s" %
(str(e), repr(handle.read()), repr(records)))
self.assertEqual(p1, records[0])
handle.close()
handle = StringIO()
self.assertRaises(TypeError, phenotype.write, p1, handle, 1)
self.assertRaises(ValueError, phenotype.write, p1, handle, "PM-JSON")
self.assertRaises(ValueError, phenotype.write, p1, handle, "pm-csv")
handle.close()
#just the generic Alphabet (default for fasta files)
raise ValueError("Need a DNA, RNA or Protein alphabet")
if __name__ == "__main__":
from Bio._py3k import StringIO
print("Quick self test")
print
print("Repeated names without a TAXA block")
handle = StringIO("""#NEXUS
[TITLE: NoName]
begin data;
dimensions ntax=4 nchar=50;
format interleave datatype=protein gap=- symbols="FSTNKEYVQMCLAWPHDRIG";
matrix
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ----
ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG
CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
;
end;
""")
for a in NexusIterator(handle):
print(a)
for r in a:
print("%r %s %s" % (r.seq, r.name, r.id))
print("Done")
print("")
print("Repeated names with a TAXA block")
count = 0
for record in iterator:
count += 1
print_record(record)
assert count == 1
print(str(record.__class__))
if os.path.isfile(faa_filename):
print("--------")
print("FastaIterator (multiple sequences)")
iterator = FastaIterator(open(faa_filename, "r"), alphabet=generic_protein, title2ids=genbank_name_function)
count = 0
for record in iterator:
count += 1
print_record(record)
break
assert count > 0
print(str(record.__class__))
from Bio._py3k import StringIO
print("--------")
print("FastaIterator (empty input file)")
#Just to make sure no errors happen
iterator = FastaIterator(StringIO(""))
count = 0
for record in iterator:
count += 1
assert count == 0
print("Done")