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src/b/i/biopython-1.63/Bio/GenBank/__init__.py   biopython(Download)
    def title(self, content):
        if self._cur_reference is None:
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("GenBank TITLE line without REFERENCE line.",
        cur_feature.location = None
        import warnings
        from Bio import BiopythonParserWarning
        warnings.warn(BiopythonParserWarning("Couldn't parse feature location: %r"
                                             % (location_line)))
        and self._expected_size != len(sequence):
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("Expected sequence length %i, found %i (%s)."
                          % (self._expected_size, len(sequence), self.data.id),
    def residue_type(self, content):
        # Be lenient about parsing, but technically lowercase residue types are malformed.
        if 'dna' in content or 'rna' in content:
            import warnings
            from Bio import BiopythonParserWarning

src/b/i/biopython-HEAD/Bio/GenBank/__init__.py   biopython(Download)
    def title(self, content):
        if self._cur_reference is None:
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("GenBank TITLE line without REFERENCE line.",
            #e.g. join(bond(284),bond(305),bond(309),bond(305))
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("Dropping bond qualifier in feature location", BiopythonParserWarning)
            #There ought to be a better way to do this...
        cur_feature.location = None
        import warnings
        from Bio import BiopythonParserWarning
        warnings.warn(BiopythonParserWarning("Couldn't parse feature location: %r"
                                             % (location_line)))
        and self._expected_size != len(sequence):
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("Expected sequence length %i, found %i (%s)."
                          % (self._expected_size, len(sequence), self.data.id),

src/b/i/biopython-HEAD/Bio/SeqIO/SffIO.py   biopython(Download)
    if handle.read(padding).count(_null) != padding:
        import warnings
        from Bio import BiopythonParserWarning
        warnings.warn("Your SFF file is invalid, post header %i byte "
                      "null padding region contained data." % padding,
        if handle.read(padding).count(_null) != padding:
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("Your SFF file is invalid, post name %i byte "
                          "padding region contained data" % padding,
            if handle.read(padding).count(_null) != padding:
                import warnings
                from Bio import BiopythonParserWarning
                warnings.warn("Your SFF file is invalid, post quality %i "
                              "byte padding region contained data" % padding,
    if handle.read(padding).count(_null) != padding:
        import warnings
        from Bio import BiopythonParserWarning
        warnings.warn("Your SFF file is invalid, post name %i "
                      "byte padding region contained data" % padding,
        if handle.read(padding).count(_null) != padding:
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("Your SFF file is invalid, post quality %i "
                          "byte padding region contained data" % padding,

src/b/i/biopython-1.63/Bio/SeqIO/SffIO.py   biopython(Download)
    if handle.read(padding).count(_null) != padding:
        import warnings
        from Bio import BiopythonParserWarning
        warnings.warn("Your SFF file is invalid, post header %i byte "
                      "null padding region contained data." % padding,
        if handle.read(padding).count(_null) != padding:
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("Your SFF file is invalid, post name %i byte "
                          "padding region contained data" % padding,
            if handle.read(padding).count(_null) != padding:
                import warnings
                from Bio import BiopythonParserWarning
                warnings.warn("Your SFF file is invalid, post quality %i "
                              "byte padding region contained data" % padding,
    if handle.read(padding).count(_null) != padding:
        import warnings
        from Bio import BiopythonParserWarning
        warnings.warn("Your SFF file is invalid, post name %i "
                      "byte padding region contained data" % padding,
        if handle.read(padding).count(_null) != padding:
            import warnings
            from Bio import BiopythonParserWarning
            warnings.warn("Your SFF file is invalid, post quality %i "
                          "byte padding region contained data" % padding,

src/b/i/biopython-HEAD/Bio/SeqIO/QualityIO.py   biopython(Download)
from math import log
import warnings
from Bio import BiopythonWarning, BiopythonParserWarning
 
 

src/b/i/biopython-1.63/Bio/SeqIO/QualityIO.py   biopython(Download)
from math import log
import warnings
from Bio import BiopythonWarning, BiopythonParserWarning
 
 

src/b/i/biopython-HEAD/Bio/SeqIO/_index.py   biopython(Download)
            except ValueError as err:
                import warnings
                from Bio import BiopythonParserWarning
                warnings.warn("Could not parse the SFF index: %s" % err,
                              BiopythonParserWarning)

src/b/i/biopython-1.63/Bio/SeqIO/_index.py   biopython(Download)
            except ValueError as err:
                import warnings
                from Bio import BiopythonParserWarning
                warnings.warn("Could not parse the SFF index: %s" % err,
                              BiopythonParserWarning)

src/b/i/biopython-HEAD/Bio/SearchIO/BlastIO/blast_xml.py   biopython(Download)
from xml.sax.saxutils import XMLGenerator, escape
 
from Bio import BiopythonParserWarning
 
 

src/b/i/biopython-HEAD/Bio/SwissProt/__init__.py   biopython(Download)
    if warn:
        import warnings
        from Bio import BiopythonParserWarning
        warnings.warn("Possibly corrupt RX line %r" % value,
                      BiopythonParserWarning)

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