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src/b/i/biopython-1.63/Bio/SeqIO/PdbIO.py biopython(Download)
# Deduce the PDB ID from the PDB header # ENH: or filename? from Bio.File import UndoHandle undo_handle = UndoHandle(handle) firstline = undo_handle.peekline()
src/b/i/biopython-HEAD/Bio/SeqIO/PdbIO.py biopython(Download)
# Deduce the PDB ID from the PDB header # ENH: or filename? from Bio.File import UndoHandle undo_handle = UndoHandle(handle) firstline = undo_handle.peekline()
src/b/i/biopython-1.63/Bio/SearchIO/FastaIO.py biopython(Download)
from Bio._py3k import _as_bytes, _bytes_to_string from Bio.Alphabet import generic_dna, generic_protein from Bio.File import UndoHandle from Bio.SearchIO._index import SearchIndexer from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
def __init__(self, handle, __parse_hit_table=False): self.handle = UndoHandle(handle) self._preamble = self._parse_preamble() def __iter__(self):
def __init__(self, filename): SearchIndexer.__init__(self, filename) self._handle = UndoHandle(self._handle) def __iter__(self):
src/b/i/biopython-HEAD/Bio/SearchIO/FastaIO.py biopython(Download)
from Bio._py3k import _as_bytes, _bytes_to_string from Bio.Alphabet import generic_dna, generic_protein from Bio.File import UndoHandle from Bio.SearchIO._index import SearchIndexer from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
def __init__(self, handle, __parse_hit_table=False): self.handle = UndoHandle(handle) self._preamble = self._parse_preamble() def __iter__(self):
def __init__(self, filename): SearchIndexer.__init__(self, filename) self._handle = UndoHandle(self._handle) def __iter__(self):
src/b/i/biopython-1.63/Bio/UniGene/UniGene.py biopython(Download)
def feed( self, handle ): if isinstance(handle, Bio.File.UndoHandle): uhandle = handle else: uhandle = Bio.File.UndoHandle(handle)
if( __name__ == '__main__' ): with open( 'Hs13225.htm') as handle: undo_handle = Bio.File.UndoHandle( handle ) unigene_parser = UniGeneParser() unigene_parser.parse( handle )
src/b/i/biopython-1.63/Bio/Blast/NCBIStandalone.py biopython(Download)
uhandle = handle else: uhandle = File.UndoHandle(handle) # Try to fast-forward to the beginning of the blast report.
"I expected a file handle or file-like object, got %s" % type(handle)) self._uhandle = File.UndoHandle(handle) self._parser = parser self._header = []
src/b/i/biopython-HEAD/Bio/Blast/NCBIStandalone.py biopython(Download)
uhandle = handle else: uhandle = File.UndoHandle(handle) # Try to fast-forward to the beginning of the blast report.
"I expected a file handle or file-like object, got %s" % type(handle)) self._uhandle = File.UndoHandle(handle) self._parser = parser self._header = []
src/b/i/biopython---popgen-HEAD/src/PopGen/Gio/PedIO.py biopython---popgen(Download)
uhandle = handle else: uhandle = File.UndoHandle(handle) consumer.start_record()
src/b/i/biopython---popgen-HEAD/src/PopGen/GenePop/__init__.py biopython---popgen(Download)
uhandle = handle else: uhandle = File.UndoHandle(handle) consumer.start_record()
src/b/i/biopython---popgen-HEAD/src/PopGen/FStat/__init__.py biopython---popgen(Download)
uhandle = handle else: uhandle = File.UndoHandle(handle)
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