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Collection of modules for dealing with biological data in Python.

The Biopython Project is an international association of developers
of freely available Python tools for computational molecular biology.

http://biopython.org

src/b/i/biopython-1.63/Bio/Align/__init__.py   biopython(Download)
        """
        import warnings
        import Bio
        warnings.warn("This method is deprecated and is provided for backwards compatibility with the old Bio.Align.Generic.Alignment object. Please use the slice notation instead, as get_column is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
        return _Alignment.get_column(self, col)
        """
        import warnings
        import Bio
        warnings.warn("The start, end, and weight arguments are not supported! This method only provides limited backwards compatibility with the old Bio.Align.Generic.Alignment object. Please use the append method with a SeqRecord instead, as the add_sequence method is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
        #Should we handle start/end/strand information somehow? What for?

src/b/i/biopython-HEAD/Bio/Align/__init__.py   biopython(Download)
        """
        import warnings
        import Bio
        warnings.warn("This method is deprecated and is provided for backwards compatibility with the old Bio.Align.Generic.Alignment object. Please use the slice notation instead, as get_column is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
        return _Alignment.get_column(self, col)
        """
        import warnings
        import Bio
        warnings.warn("The start, end, and weight arguments are not supported! This method only provides limited backwards compatibility with the old Bio.Align.Generic.Alignment object. Please use the append method with a SeqRecord instead, as the add_sequence method is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
        #Should we handle start/end/strand information somehow? What for?

src/b/i/biopython-1.63/Bio/Align/Generic.py   biopython(Download)
        """
        import warnings
        import Bio
        warnings.warn("With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is deprecated and is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
        if not (isinstance(alphabet, Alphabet.Alphabet)
        """
        import warnings
        import Bio
        warnings.warn("This method is deprecated, since the alignment object"
                      "now acts more like a list. Instead of calling "
        """
        import warnings
        import Bio
        warnings.warn("This is a legacy method and is likely to be removed in a future release of Biopython. In new code where you need to access the rows of the alignment (i.e. the sequences) consider iterating over them or accessing them as SeqRecord objects.", Bio.BiopythonDeprecationWarning)
        return self._records[number].seq

src/b/i/biopython-HEAD/Bio/Align/Generic.py   biopython(Download)
        """
        import warnings
        import Bio
        warnings.warn("With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is deprecated and is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
        if not (isinstance(alphabet, Alphabet.Alphabet)
        """
        import warnings
        import Bio
        warnings.warn("This method is deprecated, since the alignment object"
                      "now acts more like a list. Instead of calling "
        """
        import warnings
        import Bio
        warnings.warn("This is a legacy method and is likely to be removed in a future release of Biopython. In new code where you need to access the rows of the alignment (i.e. the sequences) consider iterating over them or accessing them as SeqRecord objects.", Bio.BiopythonDeprecationWarning)
        return self._records[number].seq

src/b/i/biopython-1.63/Bio/SubsMat/__init__.py   biopython(Download)
 
# BioPython imports
import Bio
from Bio import Alphabet
from Bio.SubsMat import FreqTable

src/b/i/biopython-HEAD/Bio/SubsMat/__init__.py   biopython(Download)
 
# BioPython imports
import Bio
from Bio import Alphabet
from Bio.SubsMat import FreqTable

src/c/g/cgat-HEAD/scripts/optic/prune_multiple_alignment.py   cgat(Download)
import scipy.cluster
 
import Bio
import Bio.Cluster
 

src/a/b/abstrackr-0.3.0dev/abstrackr/lib/xml_to_sql.py   abstrackr(Download)
import elementtree
from elementtree.ElementTree import ElementTree
import Bio
from Bio import Entrez
 

src/a/b/abstrackr-0.3.0dev/abstrackr/lib/pubmedpy.py   abstrackr(Download)
import os
from optparse import OptionParser
import Bio
from Bio import Entrez
from Bio import Medline

src/c/g/cgat-HEAD/scripts/nr2table.py   cgat(Download)
 
import CGAT.Experiment as E
import Bio
import CGAT.FastaIterator as FastaIterator
 

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