biana.BianaObjects.SequenceAlignment'.SequenceAlignment

Class SequenceAlignment

Object to represent a sequence alignment, multiple or not

Instance Methods

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__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

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_get_C_align(self)

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_get_aligned_sequence(self, sequence_id)

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_get_sequence_fragments(self, aln_position)

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_get_sequence_fragments_from_ascii(self, ascii_fragments)

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add_sequence_to_position(self, sequence_id, sequence_position, taxID_list=[], sequence_fragments_ascii=None, aligned_sequence=None, complete_sequence=None, crossID=None) source code

append_sequence(self, sequence_id, aligned_sequence, taxID_list=[], sim=None, wsim=None, lali=None, crossID=None)
Appends the aligned sequence to the alignment source code

append_sequence_fragments(self, sequence_id, sequence_fragments, complete_sequence, crossID=None)

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clean_empty_sequences(align1, align2)

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concatenate_alignments(self, alignment2)
Concatenate two alginments.

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concatenate_by_crossID(self, alignment2)

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get_aligned_sequence(self, seq_pos, start_pos=None, end_pos=None)

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get_alignment(self)
Returns the alignment in the following format: A list where each position contains the string corresponding to the sequence in string format

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get_alignment_length(self)

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get_number_of_sequences(self)

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get_sequence_fragments(self)

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get_sequence_fragments_by_id(self, seq_id)

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get_sequence_fragments_by_pos(self, seq_pos)

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get_sequence_fragments_in_ascii(self, seq_position)

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get_species_ordered_alignment(self, alignment2, method='only_first')
Returns an alignment object where sequence positions have been ordered according to its specie source code

get_subalignment(self, fragments)
"fragments" is a list of tuples with the format (start_position, end_position), with the fragments to select

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get_subalignment_for_sequence_without_gaps(self, sequenceID)
Returns a new alignment, in the same order, but eliminating all the positions in which sequenceID has a gap

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print_alignment(self, format='default', fd_out=sys.stdout)
Prints the alignment with the default identifier source code

set_alignment_length(self, length)

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set_number_of_sequences(self, number_of_sequences)

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set_taxIDlist(self, sequenceID, taxIDslist)

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__