def test_is_seekable(self):
"It tests wether the fhands are seekable or not"
# StringIO
fhand = StringIO("hola")
assert fhand_is_seekable(fhand)
# standard file
fhand = NamedTemporaryFile()
fhand.seek(0)
assert fhand_is_seekable(fhand)
# a wrapped BufferedReader
fhand2 = wrap_in_buffered_reader(fhand)
assert fhand_is_seekable(fhand2)
# pylint: disable=R0903
# pylint: disable=C0111
class NonSeekable(object):
"Just for testing"
pass
assert not fhand_is_seekable(NonSeekable())
class NonSeekable2(object):
def seek(self):
pass
def seekable(self):
return False
assert not fhand_is_seekable(NonSeekable2())
def test_is_seekable(self):
'It tests wether the fhands are seekable or not'
# StringIO
fhand = StringIO('hola')
assert fhand_is_seekable(fhand)
# standard file
fhand = NamedTemporaryFile()
fhand.seek(0)
assert fhand_is_seekable(fhand)
# a wrapped BufferedReader
fhand2 = wrap_in_buffered_reader(fhand)
assert fhand_is_seekable(fhand2)
# pylint: disable=R0903
# pylint: disable=C0111
class NonSeekable(object):
'Just for testing'
pass
assert not fhand_is_seekable(NonSeekable())
class NonSeekable2(object):
def seek(self):
pass
def seekable(self):
return False
assert not fhand_is_seekable(NonSeekable2())
def _get_some_qual_and_lengths(fhand, force_file_as_non_seek):
'It returns the quality characters and the lengths'
seqs_to_peek = get_setting('SEQS_TO_GUESS_FASTQ_VERSION')
chunk_size = get_setting('CHUNK_TO_GUESS_FASTQ_VERSION')
lengths = array('I')
seqs_analyzed = 0
if fhand_is_seekable(fhand) and not force_file_as_non_seek:
fmt_fhand = fhand
chunk = fmt_fhand.read(chunk_size)
fhand.seek(0)
else:
chunk = peek_chunk_from_file(fhand, chunk_size)
fmt_fhand = cStringIO.StringIO(chunk)
try:
for seq in FastqGeneralIterator(fmt_fhand):
qual = [ord(char) for char in seq[2]]
sanger_chars = [q for q in qual if q < 64]
if sanger_chars:
fhand.seek(0)
return None, True, chunk # no quals, no lengths, is_sanger
lengths.append(len(qual))
seqs_analyzed += 1
if seqs_analyzed > seqs_to_peek:
break
except ValueError:
msg = 'The file is Fastq, but the version is difficult to guess'
raise UndecidedFastqVersionError(msg)
finally:
fhand.seek(0)
return lengths, None, chunk # don't know if it's sanger
def _get_some_qual_and_lengths(fhand, force_file_as_non_seek):
"It returns the quality characters and the lengths"
seqs_to_peek = SEQS_TO_GUESS_FASTQ_VERSION
chunk_size = CHUNK_TO_GUESS_FASTQ_VERSION
lengths = array("I")
seqs_analyzed = 0
if fhand_is_seekable(fhand) and not force_file_as_non_seek:
fmt_fhand = fhand
else:
chunk = peek_chunk_from_file(fhand, chunk_size)
fmt_fhand = cStringIO.StringIO(chunk)
try:
for seq in FastqGeneralIterator(fmt_fhand):
qual = [ord(char) for char in seq[2]]
sanger_chars = [q for q in qual if q < 64]
if sanger_chars:
fhand.seek(0)
return None, True # no quals, no lengths, is_sanger
lengths.append(len(qual))
seqs_analyzed += 1
if seqs_analyzed > seqs_to_peek:
break
except ValueError:
raise UnknownFormatError("Malformed fastq")
finally:
fhand.seek(0)
return lengths, None # quals, lengths, don't know if it's sanger
def _get_some_qual_and_lengths(fhand, force_file_as_non_seek):
'It returns the quality characters and the lengths'
seqs_to_peek = get_setting('SEQS_TO_GUESS_FASTQ_VERSION')
chunk_size = get_setting('CHUNK_TO_GUESS_FASTQ_VERSION')
lengths = array('I')
seqs_analyzed = 0
if fhand_is_seekable(fhand) and not force_file_as_non_seek:
fmt_fhand = fhand
chunk = fmt_fhand.read(chunk_size)
fhand.seek(0)
else:
chunk = peek_chunk_from_file(fhand, chunk_size)
fmt_fhand = cStringIO.StringIO(chunk)
try:
for seq in FastqGeneralIterator(fmt_fhand):
qual = [ord(char) for char in seq[2]]
sanger_chars = [q for q in qual if q < 64]
if sanger_chars:
fhand.seek(0)
return None, True, chunk # no quals, no lengths, is_sanger
lengths.append(len(qual))
seqs_analyzed += 1
if seqs_analyzed > seqs_to_peek:
break
except ValueError:
msg = 'The file is Fastq, but the version is difficult to guess'
raise UndecidedFastqVersionError(msg)
finally:
fhand.seek(0)
return lengths, None, chunk # don't know if it's sanger
