Class BaseProteinAlignmentReader

object --+
         |
        BaseProteinAlignmentReader

Known Subclasses:

Base class for reading protein sequence alignments from files.

Instance Methods

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Methods

ProteinAlignment

read(cls, file_name)
Returns alignment read from file in Clustal *.aln format preserving order of sequences.

Static Methods

ProteinAlignment

_makeProteinAlignment(sequences)
Helper function that creates ProteinAlignment from a dictionary of sequence elements and list of sequence names.

Properties

Inherited from object: __class__

Method Details

Helper function that creates ProteinAlignment from a dictionary of sequence elements and list of sequence names.

Parameters:

sequences (collections.OrderedDict) - Ordered dictionary of sequence elements.
AlnClass (alignment.ProteinAlignment) - The Alignment class to use in constructing alignments

Returns: ProteinAlignment

Protein alignment.

Returns alignment read from file in Clustal *.aln format preserving order of sequences.

Parameters:

Returns: ProteinAlignment

An alignment

Raises:

Note: The alignment can be empty if no sequence was present in the input file.