Merge branch 'Eric_version_for_sequence'
Conflicts: python/obitools3/obidms/_obidmscolumn_seq.pyx
This commit is contained in:
0
python/obitools3/format/__init__.py
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0
python/obitools3/format/__init__.py
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10
python/obitools3/format/fasta.pxd
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python/obitools3/format/fasta.pxd
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@ -0,0 +1,10 @@
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from ..utils cimport bytes2str
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from .header cimport HeaderFormat
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from cython.view cimport array as cvarray
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cdef class FastaFormat:
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cdef HeaderFormat headerFormater
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cdef size_t sequenceBufferLength
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cdef char* sequenceBuffer
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32
python/obitools3/format/fasta.pyx
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32
python/obitools3/format/fasta.pyx
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cimport cython
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from libc.stdlib cimport malloc, free, realloc
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from libc.string cimport strncpy
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cdef class FastaFormat:
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def __init__(self, list tags=[], bint printNAKeys=False):
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self.headerFormater = HeaderFormat(True,
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tags,
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printNAKeys)
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@cython.boundscheck(False)
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def __call__(self, dict data):
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cdef bytes brawseq = data['sequence']
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cdef size_t lseq = len(brawseq)
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cdef size_t k=0
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cdef list lines = []
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for k in range(0,lseq,60):
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lines.append(brawseq[k:(k+60)])
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brawseq = b'\n'.join(lines)
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return "%s\n%s" % (self.headerFormater(data),bytes2str(brawseq))
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7
python/obitools3/format/header.pxd
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7
python/obitools3/format/header.pxd
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@ -0,0 +1,7 @@
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cdef class HeaderFormat:
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cdef str start
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cdef set tags
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cdef bint printNaKeys
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cdef size_t headerBufferLength
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60
python/obitools3/format/header.pyx
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60
python/obitools3/format/header.pyx
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@ -0,0 +1,60 @@
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cdef class HeaderFormat:
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def __init__(self, bint fastaHeader=True, list tags=[], bint printNAKeys=False):
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'''
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@param fastaHeader:
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@type fastaHeader: `bool`
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@param tags:
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@type tags: `list` of `bytes`
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@param printNAKeys:
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@type printNAKeys: `bool`
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'''
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self.tags = set(tags)
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self.printNaKeys = printNAKeys
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if fastaHeader:
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self.start=">"
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else:
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self.start="@"
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self.headerBufferLength = 1000
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#self.headerBuffer = []
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def __call__(self, dict data):
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cdef str header
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cdef dict tags = data['tags']
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cdef set ktags
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cdef list lines = [""]
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cdef str tagline
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if self.tags is not None and self.tags:
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ktags = self.tags
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else:
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ktags = set(tags.keys())
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for k in ktags:
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if k in tags:
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value = tags[k]
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if value is not None or self.printNaKeys:
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lines.append("%s=%s;" % (k,tags[k]))
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if len(lines) > 1:
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tagline=" ".join(lines)
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else:
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tagline=""
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if data['definition'] is not None:
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header = "%s%s%s %s" % (self.start,data['id'],
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tagline,
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data['definition'])
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else:
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header = "%s%s%s" % (self.start,data['id'],
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tagline)
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return header
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@ -26,17 +26,26 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
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if value == OBISeq_NA :
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result = None
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else :
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result = bytes2str(value)
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free(value)
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try:
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result = <bytes> value
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finally:
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free(value)
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return result
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cpdef set_line(self, index_t line_nb, object value):
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cdef bytes value_b
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if value is None :
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if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBISeq_NA) < 0:
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raise Exception("Problem setting a value in a column")
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else :
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if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
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raise Exception("Problem setting a value in a column")
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value_b = OBISeq_NA
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elif isinstance(value, bytes) :
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value_b = value
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elif isinstance(value, str) :
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value_b = str2bytes(value)
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else:
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raise TypeError('Sequence value must be of type Bytes, Str or None')
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if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
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raise Exception("Problem setting a value in a column")
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# TODO choose alignment type (lcs or other) with supplementary argument
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cpdef align(self,
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@ -62,10 +71,13 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
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if value == OBISeq_NA :
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result = None
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else :
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result = bytes2str(value)
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free(value)
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try:
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result = <bytes> value
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finally:
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free(value)
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return result
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cpdef object get_line(self, index_t line_nb) :
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cdef char* value
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cdef object value_in_result
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@ -81,8 +93,10 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
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if value == OBISeq_NA :
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value_in_result = None
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else :
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value_in_result = bytes2str(value)
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free(value)
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try:
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value_in_result = <bytes> value
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finally:
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free(value)
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result[self.elements_names[i]] = value_in_result
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if all_NA and (value_in_result is not None) :
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all_NA = False
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@ -1,5 +1,6 @@
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#cython: language_level=3
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from ..utils cimport str2bytes
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from .header cimport parseHeader
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from ..files.universalopener cimport uopen
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from ..files.linebuffer cimport LineBuffer
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@ -6,12 +6,15 @@ Created on 30 mars 2016
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@author: coissac
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'''
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def fastaIterator(lineiterator, int buffersize=100000000):
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cdef LineBuffer lb
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cdef str ident
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cdef str definition
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cdef dict tags
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cdef list s
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cdef bytes sequence
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cdef bytes quality
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if isinstance(lineiterator,(str,bytes)):
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lineiterator=uopen(lineiterator)
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@ -31,12 +34,12 @@ def fastaIterator(lineiterator, int buffersize=100000000):
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try:
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while line[0]!='>':
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s.append(line[0:-1])
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s.append(str2bytes(line)[0:-1])
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line = next(i)
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except StopIteration:
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pass
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sequence = "".join(s)
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sequence = b"".join(s)
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quality = None
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yield { "id" : ident,
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@ -1,5 +1,7 @@
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#cython: language_level=3
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from ..utils cimport str2bytes
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from .header cimport parseHeader
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from ..files.universalopener cimport uopen
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from ..files.linebuffer cimport LineBuffer
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@ -6,15 +6,13 @@ Created on 30 mars 2016
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@author: coissac
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'''
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def fastqIterator(lineiterator, int buffersize=100000000):
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cdef LineBuffer lb
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cdef str ident
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cdef str definition
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cdef dict tags
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cdef bytes sequence
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cdef bytes quality
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if isinstance(lineiterator,(str,bytes)):
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lineiterator=uopen(lineiterator)
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@ -27,9 +25,9 @@ def fastqIterator(lineiterator, int buffersize=100000000):
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i = iter(lb)
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for line in i:
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ident,tags,definition = parseHeader(line)
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sequence = next(i)[0:-1]
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sequence = str2bytes(next(i)[0:-1])
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next(i)
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quality = next(i)[0:-1]
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quality = str2bytes(next(i)[0:-1])
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yield { "id" : ident,
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"definition" : definition,
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