def test_open_ro__uncompressed():
handle = open_ro('tests/data/fasta_file.fasta')
try:
assert_equal(handle.read(),
b'>This_is_FASTA!\nACGTN\n>This_is_ALSO_FASTA!\nCGTNA\n')
finally:
handle.close()
def read_msa(filename, read_meta = False):
"""Reads a MSA from the specified filename. The file may
be uncompressed, gzipped or bzipped. See also 'parse_msa'."""
fasta_file = open_ro(filename)
try:
return parse_msa(iter(fasta_file), read_meta = read_meta)
finally:
fasta_file.close()
def from_file(cls, filename):
"""Reads a MSA from the specified filename. The file may
be uncompressed, gzipped or bzipped. See also 'MSA.from_lines'."""
fasta_file = open_ro(filename)
try:
return MSA.from_lines(fasta_file)
except MSAError, error:
raise MSAError("%s in file %r" % (error, filename))
def test_open_ro__bz2():
handle = open_ro('tests/data/fasta_file.fasta.bz2')
try:
assert_equal(handle.read(),
b'>This_is_BZ_FASTA!\nCGTNA\n'
b'>This_is_ALSO_BZ_FASTA!\nACGTN\n')
finally:
handle.close()
def read_msa(filename, read_meta=False):
"""Reads a MSA from the specified filename. The file may
be uncompressed, gzipped or bzipped. See also 'parse_msa'."""
fasta_file = open_ro(filename)
try:
return parse_msa(iter(fasta_file), read_meta=read_meta)
finally:
fasta_file.close()
def test_open_ro__gz():
handle = open_ro('tests/data/fasta_file.fasta.gz')
try:
assert_equal(
handle.read(),
b'>This_is_GZipped_FASTA!\nACGTN\n>This_is_ALSO_GZipped_FASTA!\nCGTNA\n'
)
finally:
handle.close()
def read_fasta(filename):
"""Reads an unindexed FASTA file, returning a sequence of
tuples containing the name and sequence of each entry in
the file. The FASTA file may be GZIP/BZ2 compressed."""
fasta_file = open_ro(filename)
try:
for record in parse_fasta(iter(fasta_file)):
yield record
finally:
fasta_file.close()
def read_fasta(filename):
"""Reads an unindexed FASTA file, returning a sequence of
tuples containing the name and sequence of each entry in
the file. The FASTA file may be GZIP/BZ2 compressed."""
fasta_file = open_ro(filename)
try:
for record in parse_fasta(iter(fasta_file)):
yield record
finally:
fasta_file.close()
def from_file(cls, filename):
"""Reads an unindexed FASTA file, returning a sequence of
tuples containing the name and sequence of each entry in
the file. The FASTA file may be GZIP/BZ2 compressed."""
fasta_file = open_ro(filename)
try:
for record in FASTA.from_lines(fasta_file):
yield record
finally:
fasta_file.close()
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
for record in text.parse_lines(handle, BEDRecord):
yield record
finally:
if handle:
handle.close()
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
for record in text.parse_lines(handle, BEDRecord):
yield record
finally:
if handle:
handle.close()
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
parser = pysam.asBed()
for record in text.parse_lines(handle, parser):
# Force evaluation of (lazily parsed) properties
_ = record.start
_ = record.end
yield record
finally:
if handle:
handle.close()
def read_bed_file(filename):
"""Parses a (gzip/bzip2 compressed) BED file, and yields
a sequence of records. Comments and empty lines are skipped."""
handle = None
try:
handle = fileutils.open_ro(filename)
parser = pysam.asBed()
for record in text.parse_lines(handle, parser):
# Force evaluation of (lazily parsed) properties
_ = record.start
_ = record.end
yield record
finally:
if handle:
handle.close()
def test_open_ro__gz():
handle = open_ro('tests/data/fasta_file.fasta.gz')
try:
assert_equal(handle.read(), b'>This_is_GZipped_FASTA!\nACGTN\n>This_is_ALSO_GZipped_FASTA!\nCGTNA\n')
finally:
handle.close()
def test_open_ro__uncompressed():
handle = open_ro('tests/data/fasta_file.fasta')
try:
assert_equal(handle.read(), b'>This_is_FASTA!\nACGTN\n>This_is_ALSO_FASTA!\nCGTNA\n')
finally:
handle.close()
